Broken
by shepsgirl72
Summary: AU following the events of Lifeline. Elizabeth is discovered abandoned on a desolate planet after her abduction by the Asurans. Sheppard and his team struggle to deal with the fact they left her behind and the feelings of mistrust they harbour toward her.
1. Chapter 1

**Title:** Broken

**Rating:** PG +13 (violent scenes later in the story)

**Disclaimer:** Stargate belongs to Metro-Goldwyn-Mayer Studios Inc. No infringement of any rights is intended.

**Spoilers:** Quotes from the transcripts for 'Real World' and 'Lifeline', and spoilers for numerous episodes up to and including 'Lifeline'.

**Summary:** AU following the events of Lifeline. Elizabeth is discovered abandoned on a desolate planet after her abduction by the Asurans. Sheppard and his team struggle to come to terms with the fact they left her behind and the feelings of mistrust of their former leader now evokes in them. Did the Asurans really abandon her because she was able to withstand their attempts at questioning, or is her return to Atlantis the trap they all suspect it is? The strain begins to take its toll on them as they struggle to cope with a damaged city and the dangerous situation Elizabeth's presence amongst them creates. As friendships fall apart, can they rebuild the bonds they once had, or are they forever broken?

Character death, but one presented in canon.

This story is complete apart from final editing and will be posted at regular intervals.

**Chapter 1**

_The Asurans stood frozen all around them as Sheppard and Ronon made their way back to the jumper. It was as if they'd walked into the middle of some kind of crazy 'Living Statue' mime convention, except the colonel was pretty sure these guys would do a lot more than push against an imaginary stiff wind if they got moving again. Sheppard knew this had to be down to Elizabeth and was glad Rodney's kill switch had malfunctioned. All they had to do now was find her so they could all get out of there. He activated his earpiece to contact the scientist._

'_Still nothing from Elizabeth?' he asked._

'_No. Can't communicate with her; I can't track her; it's like she just – she just disappeared.'_

'_Well, if she's the one who froze the Replicators, that means she's probably still alive,' Sheppard replied, finding some comfort in that thought._

'_For the moment, maybe,' he heard McKay reply._

'_She can't be that far,' Sheppard reiterated, refusing to listen to him._

'_We'll find her,' Ronon rumbled, adding his support._

'_Well, you'd better make it fast. These Replicators could unfreeze at any time,' Rodney told them._

_Aggravated that McKay always felt the need to state the obvious, Sheppard barked back, 'Thanks, Rodney!'_

_They ran around the next corner and stumbled right into the final stages of Elizabeth's mental battle with Oberoth. The huge Asuran was on his knees and had hold of her arm, her hand positioned as if she had penetrated his skull the way the Replicators had done to them in the past, but he had now pushed it back from him. _

'_Elizabeth!' Sheppard forced the word out, even as his throat began to constrict in panic. He could see the situation unfolding in front of him, but there wasn't a damn thing he could do to help. They were going to lose her to the Replicators, an enemy even more formidable than the Wraith._

'_Get to the jumper,' she shouted back to him, her sheer willpower the only thing standing between them and Oberoth's frozen minions. She looked so fragile compared to the huge, bulbous Asuran that it tore his heart out to admit she was right and he would have to leave her there in this facsimile of Atlantis. The place was as hostile and repugnant to him as Atlantis was welcoming, and he couldn't bring himself to back away._

'_You're coming with us,' he insisted, refusing to leave. Behind him, Ronon sent an ARG shot Oberoth's way, hitting him, but having no real effect. They had adapted already. They were defenceless._

'_I can't keep them frozen much longer!' she yelled, her voice cracking with panic._

'_We're not leaving you behind!' he shouted to her, postponing the inevitable for just a few moments longer. Something...he had to think of something._

'_If you don't leave right now, __none__ of us will get out of here, so __go__.' She turned her head slightly toward him. 'THAT'S AN ORDER!__'_

_He felt compelled to rush in and drag her away whether she'd given him an order to leave or not. But the ZPM waiting for them on the jumper meant he couldn't risk it. The city and everyone in it would die without it. He had to sacrifice the life of one to save many...even if that one life was Elizabeth Weir._

_Oberoth let go of Elizabeth's arm as the Asurans began to fire on both Sheppard and Ronon, forcing them to duck. But still the colonel could not leave. He felt Ronon catch hold of his Tac Vest and drag him away. 'Come on!'_

_For a moment or two he struggled against the huge Satedan, but with a sense of inevitability he gave in and followed him. He called out to her again. 'Elizabeth!'_

'_Go!'_

_The fear in her voice tore into him. She turned and his eyes locked with hers as the Asurans rushed forward and caught hold of her arms, restraining her. He held her gaze until Ronon dragged him out of sight..._

With Elizabeth's order still echoing in his head Sheppard woke, gasping in each panicked breath. Had he shouted her name out loud? Probably, but hopefully no one had heard him. His face was tacky and sweat soaked through his T-shirt where his back pressed against the mattress. He felt more like he'd run 10k than slept for half an hour. Half an hour. Was that really all he had managed? He sat up, swinging his legs out from under the covers to allow the air to cool them. He didn't feel ready to go back to sleep just yet.

The dream he'd woken from was the same one he'd relived time and again for the past three nights since they'd carried out the raid on Asuras, and he held out no hope it would stop recurring any time soon. Having cooled off in his air-conditioned room, his shirt now sat cold and uncomfortable against his skin, so he slipped it off and shuffled to his bathroom to freshen up, splashing cold water on his face, chest and back to relieve the burning sensation in his fevered body. He leaned on the sink and stared into the water, reliving the events of his dream one more time in his mind's eye. He'd refused to follow orders he disagreed with less than that one. Why had he left Elizabeth to the Asurans? If he hadn't hesitated – if he'd just acted instead of thinking about it – he might have saved her and held onto the ZPM, too. Of course, breaking her hold to remove her from the Replicator city would have released Oberoth and the hundreds if not thousands of Asurans she'd immobilised too soon for them to get a head start. But there had to be a way he could have saved her. He just hadn't been smart enough to think of it when he needed to – still couldn't work it out now, in fact.

He looked at himself in the mirror hanging above his sink, staring into his sunken, bloodshot eyes and fighting with the urge to smash his reflection. He didn't want to look at himself anymore; he'd let down one of his best friends, and he couldn't imagine how he could face that truth day after day. But smashing the mirror wouldn't bring back Elizabeth, and neither would it appease one iota of the sense that he'd betrayed her. He would simply have to find a way to cope somehow.

The worst thing was knowing he had flown her straight into enemy hands. He and his team had talked her into a heist that was always going to put her at high personal risk, and now, not only was Elizabeth in the clutches of the Replicators, but also all the knowledge of Atlantis she held, which, quite frankly, was a frightening amount. There was no way Elizabeth would be able to resist their mind probing forever, even with the enhancements of her operative nanites. Actually, all it would take would be a little reprogramming and those damned nanites would probably make her tell them everything she'd ever learned about the city and the Ancients, and about the effectiveness of their defences. Their best hope was that Oberoth had been so enraged by her actions that he'd killed her outright, and even that didn't bear thinking about. Nausea churned in his stomach, and, deciding he didn't even want to try to sleep anymore, he pulled on his trousers, boots, and a clean T-shirt and headed for the Mess hall.

The corridors were silent except for the background hum of Atlantis itself. Most personnel were tucked up in their beds asleep – all except the skeleton crew required to keep an eye on things overnight, and the scientists taking shifts to repair everything damaged in the Asuran attack and other systems that seemed to be simply giving up the ghost after the strain of their escape. He kind of liked the city when it was quiet like this. At night, he felt his connection to the place so much more clearly; it almost vibrated through every cell of his body, telling him he was meant to be there, that all the events of his life – both good and bad – had been designed to culminate in his decision to travel to this lost city. His life on Atlantis had felt complete, but with each loss, a little bit of that fulfilment ebbed away from him, and now, even alone and enjoying the way the city sang to him, it just didn't feel the same any more. He really needed to get to the Mess hall and drown his sorrows in coffee.

All the way there he kept focussing on how good it would feel to grab a drink and sit out on the balcony area in the cool night air, just relaxing and trying to empty his mind of the problems their bustling daytime hours threw at him. He still felt uncomfortably sticky and knew getting some fresh air was exactly what he needed to feel refreshed...physically if not mentally.

Unfortunately, his plans for caffeine and solitude were dashed the moment he walked into the Mess hall. Rodney was already there, sitting at one of the tables nearest the counter, head buried in his laptop as usual. The subdued evening lighting meant he was partially hidden in shadows, but his laptops screen illuminated the tiredness etched into his features, painting his face with a sickly pallor.

For a second or two, Sheppard considered heading straight back out and foregoing the drink, but he wasn't quick enough. McKay spotted him before he could perform his strategic retreat.

'Sheppard. Couldn't sleep either, huh?'

The scientist looked pleased to see him, and he didn't have the heart to walk away. With a sigh, he headed to the percolating coffee pot, helping himself to a mugful. Rodney had clearly made enough to keep himself going for a few hours; Sheppard supposed even _he_ wouldn't mind sharing one cup with a sleepless friend.

He trudged heavy-legged to the table where Rodney was working and slid into the seat opposite him, slouching as he watched his friend work. 'What's keeping you up?'

'Oh, I'm just doing some more power calculations to work out what additional defensive and offensive tech we can bring on-line thanks to the new ZedPM...once we've carried out all essential repairs that is. I swear something else trips out every hour.'

Sheppard nodded. 'Yeah, that might be wise.'

'D'you think they'll come after us?' Rodney asked, his face as devoid of irritation as Sheppard had ever seen it. Perhaps even McKay got too tired to rant sometimes.

'I'd say that's a given,' Sheppard admitted. 'But we do have one thing in our favour. They don't know for definite where we jumped to once we got the hyperdrive working. And Pegasus is a big galaxy...'

'That's two things,' Rodney pointed out.

Sheppard let that slide; he had neither the energy nor the inclination for their normal banter. He was just glad Rodney didn't seem to share his worry that Elizabeth might tell the Asurans where they were headed if probed by Oberoth, although that could just be the dulling effect of utter, mind sapping fatigue. Right now, with Atlantis in no condition to make another trip through hyperspace, all they could do was sit tight and hope the replicators didn't turn up to finish the job they'd started. No point in telling people they were sitting ducks.

'Anyway we know the attack code was activated. They're going to be busy with the Wraith for a while,' the scientist said with just a hint of smugness that irritated Sheppard more than usual.

Sucking in his cheeks, Sheppard held back the urge to list Rodney's previous failures, but knew it was time to bring Rodney down to Earth...or rather M35-117 where they currently resided. 'And you think they can't do anything else while they're doing that? We already know how tampering with their base code backfired once before. Those nanites are way beyond our current understanding and I think it's about time we acknowledged that. We need to concentrate on other ways of dealing with them...once the Wraith are defeated, of course.'

McKay looked embarrassed, his eyes darting about and seemingly unable to settle on any one thing. 'I know I've said this before, Sheppard, but I'll say it again. I'm sorry for turning the nanites back on.'

Sheppard lifted his tired, dry eyes to his friend's, seeing the sincerity in Rodney's sad face, even if he couldn't meet his eye. He hadn't meant that when he'd made the comment, at least not consciously. But, if he was completely honest with himself, he _was _still furious with Rodney for reactivating the damned things. They'd discussed it, and he'd told him not to do it unless he was absolutely certain they could repair Elizabeth's injuries and then be turned off again so they posed no further threat. But Elizabeth's condition had rapidly deteriorated, he hadn't been around to act as the voice of reason, and Rodney had panicked. It was understandable, but his mistake had both helped and hindered in so many ways it left the colonel uncertain how he should really feel. Right now, he was battling the almost irresistible urge to smack Rodney upside the head for not following his orders, yet, at the same time, he knew he'd broken so many orders and rules himself in the past few years it would be nothing short of hypocritical. But they'd lost Elizabeth, one of the best friends he'd ever had, and somewhere inside he felt a gulf had opened up he could never hope to fill.

'It's okay, Rodney,' he ground out, knowing that was what McKay needed to hear. 'You couldn't have known how this would all end...and we did get the ZPM we needed. Your actions ultimately saved a lot of lives.'

'And so did your decision to leave Elizabeth behind. So, when are you gonna stop beating yourself up over that?'

Rodney was a far more insightful man these days than he had been at the beginning of their expedition, though his diplomacy still left something to be desired. Sheppard had chosen to work with him because he was commanding Atlantis' primary team and he wanted the best people with him. But there had been several times in those early days when he'd questioned that decision. He'd rarely worked with none military personnel prior to this posting, and McKay's constant whining and pessimism had taken some getting used to. The loss of Ford had been the man's first mellowing point, and Carson's death a few weeks ago had hit him hard since the two had become firm friends in their three years together – despite their constant badgering of one another. Elizabeth's loss would be another stepping-stone in his development – a humbling one once the dust had had time to settle, he hoped.

'I keep asking to mount a mission to go back and extract her, but the IOA are stonewalling any requests I put through. I can't believe they're unwilling to see what a risk leaving her in enemy hands is,' Sheppard sighed, swirling his drink in the mug he clutched.

'Perhaps they weighed up the odds and thought the threat we face now wasn't as bad as the potential danger of several of us ending up in enemy hands,' Rodney pointed out, his voice a little squeaky as if he was afraid of how Sheppard would react to his statement. 'Not wishing to toot my own horn here, but if they caught me, this place would be in serious trouble.'

Though he knew McKay was right, his lack of modesty didn't help the way Sheppard was feeling right now. 'Whose side are you on, McKay?' he demanded, staring his friend down.

No doubt still remembering how close he'd come to a take-down when he'd refused to shut off Elizabeth's nanites, Rodney dropped his gaze to his laptop in an effort to appear less confrontational. 'Yours, of course,' he insisted. 'And you know I'll be right there the minute they give you a green light to go after her.'

Sheppard huffed, looking out of the window. 'Yeah, well, I don't think that's gonna happen any time soon,' he grumbled, taking a swig of coffee. He grimaced as it hit the back of his tongue. He was a fan of strong coffee, but Rodney's recipe was enough curl the hair on his chest. 'I think our best chance is to wait until they choose a new commander for Atlantis, then I'll appeal to whoever that is directly. Maybe they'll bend a few rules for me.'

'Any idea when that will be?' McKay asked.

Sheppard shrugged. He suspected Rodney was harbouring hopes the IOA might choose him, but he doubted they would. Rodney's reputation for tantrums and his overwhelmingly underdeveloped people skills pretty much ruled him out. 'The IOA are so bound up with red tape I doubt even they know yet. That said, I don't think they're gonna want to leave me in charge for too long. I'm not exactly their blue-eyed boy.'

'Yeah, well, they don't know you the way we do,' Rodney muttered. Shockingly, the colonel realised that was pretty damned close to a compliment, and he had no idea how to respond. He ignored it; it seemed the easiest thing to do for both of their sakes.

'Well, it's business as usual until they send through the newbie,' Sheppard said by way of a change in topic, yawning and stretching his tired limbs before clasping his hands behind his head. 'Tomorrow, we head out on yet another reconnaissance mission to seek out more allies and ZPMs.'

'Well, one of these days we have to get lucky, right?' Rodney said, giving him a lop-sided smile that faded far too quickly.

'We're lucky to survive each day, Rodney. An extra ZPM would be like all our Christmases coming at once.'

'That's true. Could you imagine the ways in which we could boost our defences if we had all that extra power in the system?' Rodney beamed, his face literally lighting up at the thought.

Sheppard could see he'd ignited the scientist's enthusiasm and decided this might be a good time to bow out of the conversation. 'Well, my bed is calling to me, so I guess I should head back to my room and try to get some rest.'

'Yeah, okay. I might just do some work on the best systems to boost if we ever do lay our hands on that elusive second ZedPM. I'll see you in the morning.'

'Don't stay up all night, Rodney. Remember we're out on reconnaissance tomorrow.'

'Another hour tops, I swear,' Rodney said dismissively, and Sheppard knew that was a lie, but let it go. Rodney was probably having as many nightmares about what he'd done as he was, so he couldn't blame him for trying to distract himself with work.

He meandered his way out of the Mess hall, and took a transporter to another part of Atlantis, one where he was unlikely to be disturbed. Then, he found that nice, quiet spot he'd been hoping to find out on one the city's east pier and sat down to enjoy the stars and the cool breeze that ruffled his hair and brought his follicles to rigid attention. He didn't mind being cold for a while; it beat waking up in a fevered sweat every few hours. Sitting down to dangle his feet over the edge, he ran over the scenario on Asuras yet again, certain he'd missed something vital he could and should have done to help.

So many things had gone wrong with that mission it was a miracle any of them had escaped Oberoth's clutches. He supposed he should be grateful he'd managed to get Ronon and Rodney out of there so they could live to fight another day. But until he got clearance to go and look for Elizabeth, he felt like he was caught in Limbo, neither completely entrenched in the world that existed prior to losing her, nor comfortable about the thought moving on without her. Atlantis had been Elizabeth's vision; she'd been the one to push it through, and the one who had fought so hard to stay and lead it. Now she was gone, and he didn't know what to do. He knew it wasn't really his fault the enemy had taken her, but at the same time he felt it was. This had all happened at a time when he was in charge of Atlantis; the responsibility for any mishaps fell squarely on his shoulders as far as he was concerned.

He lay back on the metal pier, feeling the ridged, solid metal press into the skin of his back through his thin black T-shirt. It was cold and uncomfortable, yet despite that, he soon felt himself succumbing to the pull of restless slumbers...


	2. Chapter 2

_Elizabeth sat beside John on the pier, her legs swinging casually over the edge as she gazed out across the ocean, a breeze gently lifting her brown locks away from her slender neck and shoulders._

_She smiled as she squinted into the rising sun. 'You did good, John. Snatching that ZPM was risky, and then managing to land the city without a single loss of life was nothing short of amazing – you must be very happy.'_

_John watched her take a sip from her mug of coffee, happy just to share this quiet time with his friend, but for some reason, something felt out of place. He tried to ignore the feeling, putting it down to delayed nerves. He hadn't believed they would all make it out in one piece, in fact, as he tried to remember how they'd got away he had trouble recalling it, as id squinting at the memories through opaque glass._

'_I guess so. Crazy thing is I had this nightmare about losing you to the Asurans. I'm happy that wasn't real,' he said softly._

'_Oh, you don't get rid of me that easily, John Sheppard,' she joked, nudging her shoulder into his. 'This place is my home now. Wild horses couldn't drag me away, so a few angry Asurans are definitely no match!' She smirked in the playful way she always did, sipping again from the mug of coffee she cradled between both palms._

'_It's a beautiful morning,' John commented as the rising sun painted the sky with broad strokes of orange and lilac. A warm breeze ruffled his hair, bringing welcome heat to his cold skin. 'Can't wait to get some time to explore the mainland...although we'll have to look out for those big snakes McKay mentioned.'_

'_Hmmm, I know what you mean. Being cooped up in the city is all well and good, but it's nice to feel solid ground under your feet now and again,' she mused, tilting her face up to the sun and closing her eyes as its rays caressed her._

_John looked down at his boots hanging over the water, still feeling inexplicably uneasy. 'I don't know. I kind of like the city. It feels safe,' he murmured, trying to recall how they both now found themselves sitting out on this pier. It wasn't the usual spot they chose to conduct their conversations. In fact, he didn't think they'd ever been there together before._

_Elizabeth looked toward him now, her eyes bright in the increasing light. 'Well, with your genes you have more of a connection to this place than any of us, so I suppose that's only natural.'_

'_I suppose...'_

_He looked up to the sky again, enjoying the burgeoning warmth of the morning, the dual moons now fading in the blue sky. There were five moons in total; Sam Carter had told him so...but he couldn't place when and where they'd had that conversation. When he tried to bring it to mind it became more hazy and vague, just as their escape from Asuras did._

_A dot in the vast expanse of sky caught his attention; he shielded his eyes against the sunlight and squinted at it, trying to discern its shape._

_Elizabeth saw it, too. 'What is it?' she asked, the smile slipping from her face._

'_I don't know. I see something up there, but I can't tell what it is.'_

'_Could it be some type of bird?'_

_He shook his head. 'I don't think so. It's too big. We should head inside and see what the scanners can pick up.'_

_Elizabeth caught hold of his wrist, stopping him before he could stand. 'Wait a while, John. If there's anything to worry about, someone will let us know. Let's enjoy the peace and quiet a while longer. It's so rare we get time like this I want to make the most of it.'_

_John frowned back at her, his nagging feeling of unease growing stronger now. That was a dumb idea; Elizabeth was smarter than to ignore something like this. In the Pegasus Galaxy, even the most innocuous thing could prove life threatening, they'd learned it a dozen times over at least. 'No, I really think we should get inside,' he insisted, trying to pull his arm free._

_Her grip on him tightened. 'You don't need to tell anyone, John. It would be better if you didn't.'_

_He didn't understand what she could possibly mean, and her enduring serenity in the face of potential danger disturbed him. 'Let go, Elizabeth. I have to go to the Control room in case whatever that thing is has evaded our systems somehow.'_

'_It has. They have the same technologies as the Ancients, after all, so it's easy for them to know how to avoid detection. And they have a lot more ZPMS, although they're minus one now, thanks to you.'_

'_The Asurans?' he breathed, 'How can they have found us so fast?' _

'_Because you never really left.'_

_The deep voice of Oberoth resonated in Sheppard's eardrums, and Elizabeth morphed before his eyes, taking on his bloated form. He thrust his hand into Sheppard's head, forcing a scream from him as he felt his mind turn to pulp..._

'_GO!'..._

Elizabeth's final instruction echoed though Sheppard's aching head again as his eyes snapped open to the sight of acres of blue sky.

'_Colonel Sheppard.'_

This time, it was Teyla's voice he could hear. He tried to rise, swaying as he straightened up on the end of the pier he'd fallen asleep on, gripping the edge to stop himself toppling forward.

He was alone. No Elizabeth, and no Teyla either.

'_Colonel Sheppard...John...please respond.'_

With the fog of sleep now clearing from his brain, he realised the voice was coming through his earpiece. 'Teyla, this is Sheppard. What's wrong?'

'_Nothing now that I've found you. You were not in your room and I wasn't able to locate you anywhere else. I was worried...We were about to scan for your transmitter.'_

He felt guilty for troubling her. Elizabeth's failure to return with them had struck them all hard, but Teyla had been the most visibly shaken by it. She didn't feel the need to hide her feelings the way he, Ronon, or Rodney did. He suspected she felt that if she'd been there helping them on the heist, things might have ended differently. He wondered if that meant she blamed him for asking her to remain behind. No, this was Teyla. She was nothing if not fair. She understood why he'd asked her to remain and take care of Atlantis if they didn't return. He trusted her implicitly, and he hoped she felt the same way.

'I decided to get some fresh air...' he said, still distracted by his nightmare as he scoured the skies, worried there might be something lurking out there.

'_Well, Ronon, Rodney, and I are about to take some breakfast and wondered if you would care to join us before we embark on our mission.'_

A black dot against the blue distracted Sheppard and set his heart thundering against his ribs, his breathing catching in his throat. _Oh, God. They've found us! _Thankfully, the gentle flap of wings and an elegant swerve told him it was nothing more than one of the native creatures of this new planet they found themselves on.

'_John?'_

'Er, yeah,' he replied, only now remembering Teyla had asked him a question. 'I need to shower first, so I'll meet you there in fifteen.'

'_Very well. I will let the others know.'_

Sheppard stood up and looked at the spot Elizabeth had occupied in his dream. For just a few moments there he had almost believed that she'd made it back with them, and now he felt as if he'd lost her all over again.

Checking the sky one last time, he made his way back inside to freshen up and join his team.

He took the transporter back to the level where his quarters were located, and, after a brisk two-minute walk, he was searching through his drawers for clean underwear socks and trousers. His T-shirt, which he'd only worn for a few hours, still looked clean so he decided it would do for the day.

The warmth of the shower was pleasant on his cold back, still chilled from its time lying on the metal pier. It was hard to believe he'd managed to fall asleep in such an uncomfortable place, but that was how fatigue got you sometimes. He'd slept in some pretty inhospitable surroundings out of necessity in Afghanistan amongst other places, so he knew that only too well. He felt himself begin to sway and steadied himself with a hand against the glass, closing his eyes as he let the water run freely over his face to wash away the lingering tiredness that still tugged at his eyelids. When he opened them again he thought he saw the blurry outline of a mountainous man through the steamed up glass, someone with a silhouette exactly like Oberoth's. He gasped, throwing open the door to the sight of an ancient cell. He hadn't escaped...they were still on Asuras.

Sheppard woke as his head bumped against the glass of the shower wall. He'd fallen asleep and gone straight into a nightmare so believable it took him a few moments to decide whether this was reality or not. He pushed open the shower to check the room beyond. This time it was just his bathroom; he really had momentarily lost consciousness, nothing more. Figuring the shower wasn't helping as much as he'd hoped it would, he jumped out and dried off, dressing quickly and heading back out into the corridor. Maybe coffee and muffins would succeed where the hot water had failed.

When he reached the Mess hall to collect some breakfast, his hair still damp from his ablutions, he spotted Rodney, Ronon, and Teyla sitting at the table he and McKay had occupied in the early hours for their chat. In fact, Rodney was still in the exact same chair...

He grabbed the anticipated meal and joined his friends. 'McKay, please tell me you went to bed last night,' he grunted, pulling out the chair opposite him and dropping into it as if his legs were reluctant to hold him up any longer.

Rodney's dilated pupils met his, but only for a fraction of a second. 'Of course I did. I told you I would, didn't I?' he lied, pushing food around his plate with erratic, aggressive pokes and prods of his cutlery.

He was clearly wired on caffeine, his hands trembling as he lifted his fork to his mouth to shovel in some bacon.

'We have a mission today. I told you to get some rest,' Sheppard replied, proof if Rodney needed it that he didn't believe him.

'I'm good. I just took a couple of pep pills, so that should see me through. Anyway, you're not exactly looking bright eyed and bushy tailed yourself this morning.'

'He's right, Colonel. You _do_ look tired,' Teyla agreed. Ronon just regarded him in silence as he pushed a whole pancake into his mouth and chewed it up.

'Okay, I'll admit, I'm not feeling all that good, but I did at least get some sleep last night.' _Not that I'm about to tell you it was out on a pier._

'Perhaps we should postpone the mission until you have both had more rest,' Teyla suggested, her face a picture of concern as she looked between the two of them.

'No!' they both responded in unison, looking at each other in slack-jawed shock.

Sheppard knew why they had both answered that way; it was because they both needed something to occupy them and keep their minds off Elizabeth's plight.

Ronon's eyebrows lifted a shade, but he still made no comment.

Teyla gave them both a knowing look. 'It was just a suggestion. If you really want to go ahead as planned, then, of course, we should.'

'Good,' John muttered, tucking into his breakfast with gusto. His several nights of disjointed sleep and corridor wandering had left him with a voracious appetite, and he didn't want to go on this mission hungry. That would only add to the misery of trying to stay awake. He needed calories to keep him upright.

'So, I was thinking, after this mission, my time might be better spent helping with the repairs to Atlantis. We sustained some serious damage and although we have some good people working on it, I have a much better grasp of this place than anyone else,' Rodney babbled. 'I mean, any of the military teams can carry out these reconnaissance missions, but...'

'But you're the only one capable of getting Atlantis fully functioning?' Sheppard mumbled through his food.

'Well...yes, actually. And I might need your help to re-initialise stuff, so, I need you to stay on base,' he added wagging his finger in Sheppard's direction. 'You can't expect me to sit around waiting for hours on end when there's so much work to be done.'

'Doesn't sound like much fun for me and Teyla,' Ronon pointed out, breaking his silence at last.

'Doesn't sound like much fun for me, either!' Sheppard protested, 'So you get to work on science stuff that get's you all hyped, and we have the pleasure of sitting around watching just in case you need me to touch something.'

'Look we made it here, but systems are crashing as we speak, and until we fix things we're stuck here with no choice but to hope no Wraith or Asurans come calling. And we've never really taken the time to test this city's full potential. This is probably the most time I'll ever have to research the Ancient databases to see if there are any ways of boosting our defences. Personally, I can't think of a better way of spending my time while we're –'

'While we're in hiding from our enemies and desperately trying to find more ZPMs to make us a match for them if they come after us?' Sheppard finished for him.

'No. I was going to say while we can't take any major action because we're waiting for new leadership. Look, when we first came to the Pegasus galaxy, we were supposed to explore and gather as much information about the Ancients as we could. This was never supposed to turn into a war – Elizabeth saw this as a voyage of discovery and I thought it would honour her memory if we spent some time...discovering stuff.'

'We don't know she's dead yet,' Sheppard growled, 'and the first chance I get to launch a rescue mission, I'm out of here.'

'We will all be with you,' Teyla said calmly. 'We all want to see her back as much as you do.'

'No. Apparently, some of us just want to _honour her memory_...' Sheppard spat, throwing Rodney a dirty look. This questioning of his decisions was wearing pretty thin. He really didn't have the patience to deal with Rodney right now.

McKay rolled his eyes, dropping his cutlery to the table. 'Oh, come on. You know I didn't mean I was giving up on her. I'll be right there with the rest of you when we get clearance to go. But Elizabeth wouldn't want us to put our work here on hold until she gets back.'

'Fine,' Sheppard grunted. 'You stay here and do all the repairs and discovering stuff you're itching to get involved in. Ronon, Teyla, and I can manage reconnaissance without you for a while, 'cos, you know what, I'm pretty sure Elizabeth would agree that stuff's important, too.'

'But –'

'I promise if we see any cool scientific stuff we think would float your boat, we'll bring it back with us,' Sheppard assured him. 'I hate to break this to you, but important as you no doubt are here, you are not completely indispensible out in the field.'

Ronon grinned inanely as he chewed up another pancake. Rodney just stared back at Sheppard, looking distinctly crestfallen. 'How do you know you won't miss something significant?'

'Because, contrary to popular belief, we're not that dumb!' Sheppard snapped.

Rodney picked up his fork and pushed his food around some more. 'I still think I should come with you.'

'Thought there was stuff you wanted to do here,' Ronon rumbled, smirking at him as he popped some fruit into his mouth.

'There is, but Zelenka could do it.'

'You said _you_ were the only one who could do it,' Ronon reminded him.

'Well, if I have to decide between the two things, then my place is obviously with the team,' McKay grouched.

'Obviously,' Ronon repeated, pinning him with one of his unwavering stares.

It suddenly occurred to Sheppard that there might be a very different reason for Rodney trying to keep them there on Atlantis and not wanting the team to go out without him. He'd assumed it was purely his arrogance raising its ugly head as it often did, but he saw through the act now, realising the truth was very different. Rodney was afraid of losing them. First, they'd lost Aidan, then Carson, and now Elizabeth. Their friend was clearly terrified that if he let them out of his sight, he might not see them again. Sensing his friend wouldn't appreciate having the truth exposed in such a public arena, Sheppard kept his eureka moment to himself.

Feeling bad now for giving Rodney a hard time, the colonel kept up the facade by making a joke that it was pointless continuing the argument because Rodney was never wrong. Then he finished up his meal, and arranged to meet them all in the jumper bay in one hour. Hopefully, by then he would be firing on all cylinders and Rodney would be acting more like his usual churlish self.


	3. Chapter 3

Sheppard had geared up and now stood on the balcony where he and Elizabeth did most of their thinking. Or rather, had done most of their thinking. That wasn't going to happen today, or any day soon if the IOA kept refusing to discuss his requests to go after her.

The view was different on the new planet, but just a breath taking and as calming at the one he had become so familiar with back on Lantea. The waves glistened around them, the sea barely moving in the tranquil atmosphere. This morning it looked like a Utopian paradise, if you forgot about the snakes and lonospheric storms. Elizabeth would have loved this place. It was a perfect view to help you unwind and think things through. His thoughts drifted briefly to the sight of her ordering him to leave her, but he pushed the image out of his mind, unwilling to face it unless forced on him by unwanted nightmares.

What he couldn't understand was why the IOA couldn't see that the benefits of retrieving Elizabeth from the hands of the Asurans far outweighed the potential risk of the attempt. She knew too much about Atlantis and Earth, and the longer she remained their captive, the more unlikely it was she would be able to hold out against them. He suspected they thought she was already lost, but he knew the Asurans were too smart to waste a tactical advantage that way. She was still alive; he was certain of that now, but in what condition?

The space beside him felt like a gaping canyon, the energy of her presence conspicuous by its absence. They would never find anyone capable of completely filling Elizabeth's shoes, no matter who the IOA sent out to join them on Atlantis. Elizabeth had made it her business to get to know everyone in that city, to learn their strength and weaknesses, their likes and dislikes; that kind information took a long time to gather. And who was going to rein him in the way she did? She'd always let him have his say, but then made sure he'd listened to her view, too, so they could make balanced decisions. That was her strength, and one not everyone shared. He'd been completely comfortable speaking to her, never felt the need to hold back because, above all else, he knew she respected him in a way no one else ever had. What he'd done in the past didn't matter to her. He could speak to her, and he'd always known that even if she disagreed, she would listen. He dreaded to think what misfit the IOA would choose to lead them.

He yawned, his eyes still feeling dry and heavy. He could have quite happily crawled back into bed, but the thought of what nightmares awaited him there meant he would resist the urge. Instead, he headed to the infirmary and see what Dr Keller could offer to keep him awake.

She was busy working on her laptop in her office when he got there, so engrossed in her files she didn't even hear his approach. When he cleared his throat to alert her to his presence, she almost jumped straight out of her chair.

'Oh, Colonel. You scared me,' she chuckled, pressing her hand to her chest. 'I'm sorry. Have you been waiting long?'

'No, just got here.'

She stood up, but didn't seem to know whether she should approach him or not. 'Is there something I can do for you?'

'My head's jackhammering and I feel like I need a pick-me-up...you know, something to keep me going for the mission today.'

'You're the second person to ask me for some pep pills today. I took some to Rodney in the canteen earlier. Couldn't get him away from his computer long enough to examine him here. How are you feeling?'

Sheppard stared at her, wondering just how she was pitching that question. 'I'm good...other than the headache and tiredness.'

'Are you getting much sleep?'

Her brown eyes stared back at him, wide and innocent, but no doubt masking the fact she could already tell he wasn't sleeping well. If this had been Carson asking the question, maybe he would have felt inclined to divulge his problems, but Keller...he just didn't feel able to open up to her, most likely because he was still harbouring some anger toward her because of what had happened to Elizabeth. Activating the nanites had been her idea; Rodney would never have done it if she hadn't brought the possibility to his attention. Sure, Elizabeth would have died in the infirmary that day, but at least she wouldn't have fallen into enemy hands, endangering all of them. Not that that was what bothered him most; the thought of what those replicators were doing to his friend was what kept him awake at night. But could he really be angry with the doctor? Keller's job was to save people at all costs. She'd been faced with the prospect of losing a patient and had found a solution to avoid that. That was what she had been hired to do.

Much as he wanted to tell her to stay out of his business, he knew Keller was only showing an interest in him the way any good doctor would. He had to put what she'd done behind them if they were to function together on a professional level. 'Not as much as I'd like,' he admitted, omitting the fact he was experiencing nightmares. She didn't need to know that.

'It's understandable. You've suffered a terrible loss...we all have. I understand how you feel –'

'Do you?' he heard himself snap, without even meaning to say it.

Keller pressed her lips shut, clearly unsure whether she should speak again.

Backing down, Sheppard rubbed hard circles on his temples to alleviate the pain. 'Sorry. It's this damn headache. I didn't mean to yell.'

'That's all right,' she replied, giving him a faltering smile. 'The pressure's getting to most people I know right now...' Her eyes remained fixed on his, and he could tell there was something else she wanted to say, but didn't dare. Eventually, taking a deep swallow, she spat it out. 'I think it might be an idea for you to talk your feelings through with Dr Heightmeyer...she's pretty busy right now, but I'm sure she'd find some time in her schedule to see you, you know, considering your position on Atlantis.'

Sheppard slowly counted to ten in his mind to ensure he didn't throw out his first knee-jerk reaction to that suggestion. 'It's only been three days since we lost Elizabeth and almost lost the city. I'm pretty sure it's normal to lose a little sleep over something that big.'

'It is,' she nodded emphatically. 'And the day even military personnel stop caring about losing their friends is the day they should probably give it up. Look, all I'm saying is, I can keep giving you sleeping pills and stimulants and artificially getting you through this, but you should consider whether you need a more long-term solution. Kate can offer you that.'

Sheppard figured she could tell how he felt about that idea just from the way his stance stiffened. 'I'll bare it in mind,' he mumbled, knowing he had absolutely no intention of following through on that. He'd lost enough people in his military career to know how to get himself through this.

Giving him a nervous smile, Keller scurried away to retrieved the Modofanil he needed, returning to press the pills into his waiting palm. 'You do know what happened to Elizabeth wasn't your fault, don't you?' she asked, a distinct quiver in her voice.

_Not mine alone, no, _he thought, but he didn't say it out loud. If Keller was comfortable with the actions she'd taken, who was he to rock her happy boat? Realising he was making her nervous with his broodiness, he tried to given her a more upbeat answer. 'Yeah, I know that,' he replied, although the sadness in his tone didn't even convince him. 'Elizabeth made the choice to act herself. The worst thing is she put herself in danger as if she thought she wasn't as important as us any more...like she was broken so it didn't matter if she died.'

Keller's mouth, normally fixed into an inane smile, drooped instantly. 'She knew the mission was dangerous, Colonel. You all put your lives on the line to save the city, and I'm sure she would have made that choice whether she felt that way or not. I'm very grateful she made that sacrifice. I doubt we would be here having this conversation if she hadn't.'

Sheppard once again bit back the urge to point out Keller had been the one to go against his orders and put Elizabeth in the situation where she was the only one with the ability to stop the Asurans, thus leaving their leader with little choice but to go on her suicide mission. 'I know that,' he replied, his voice low and quiet, but tinged with venom. 'But I still don't like leaving people behind.'

Keller's eyes widened. 'Okay...well, if you need anything else, you know where I am.' She reached out and squeezed his arm, reminding him of his dream out on the pier. He resisted the urge to shake her off, instead waiting for her to move on before throwing back his pills and heading out to the jumper bay. Hopefully they would keep him alert enough to pull this mission off to McKay's satisfaction or he'd never hear the end of it.

*****

The rest of his team were talking quietly amongst themselves when Sheppard reached the jumper, and the chatter stopped as soon as they saw him approaching. He supposed he'd been the main subject of their conversation, but didn't have the energy to ask if that was true or to feel annoyed.

'Let's go, people,' he ordered, pushing past them to stride up the rear ramp and take up the pilot seat.

Teyla slipped into the seat beside him, and from the corner of his eye, he could see her watching him intently. He hoped she wouldn't say anything, but Teyla was the type who simply couldn't help but voice her concern for her friends. 'Are you sure you are well enough to do this journey, John? You look exhausted.'

'Flying doesn't take that much effort,' he said with a shrug, 'and the meds I just got from Keller to keep me alert will kick in soon. Besides, I can rest when we get back.'

'If you are certain you can manage,' she smiled sympathetically.

'Are you kidding? I can fly this thing with my eyes closed.'

'Looking at you, I'd say that's a good thing,' Ronon quipped, giving him a broad grin.

Sheppard sighed and turned his seat to face him. 'Look, I admit I'm tired, but I'm not about to fall down just yet. I've managed with far less shut eye than this before.'

'We know you would tell us if you didn't feel able to cope,' Teyla assured him. Sheppard looked back at her, her deep brown eyes holding his gaze in a way that made him realise she wasn't talking about just the mission. It was an attempt to communicate greater concerns that she knew he wouldn't wish her to raise overtly. At least she had the insight to be tactful about it.

He nodded and got on with the job of prepping the jumper for launch. He could feel Teyla still watching him as he did it, but didn't acknowledge the fact. He wasn't ready to admit he was struggling to cope with the loss of Elizabeth just yet. They were at war, and in times of war there were always casualties. Elizabeth had given her life so others could live, and to mourn her openly would belittle that sacrifice. She'd made the choice to stay and hold the Asurans at bay long enough for his mission to be successful. He had to give the impression that he admired and appreciated the tactical advantage she'd given them, even if it actually made him angrier than he had ever felt in his life. Was he mad at Elizabeth, too? Yes, he supposed he was – mainly because he truly believed she'd considered her life forfeit because she was no longer a 'perfect' human.

He started the engines and lowered the jumper down into the gate room. The 'gate was already active and waiting for them to fly through it, the brilliance of the rippling surface making him squint as he brought the jumper to a halt before it. In his mind, Sheppard heard Elizabeth's voice say, _Be safe._

He didn't need the hollow echoes of his friend's concern to tell him that. The three colleagues with him were the three people he felt closest to in the galaxy...in two galaxies, in fact. He would keep them safe at all costs, even if that meant making the same sacrifice Elizabeth had for Atlantis. He was prepared to do that for them – now more than ever.

He set the jumper in motion, breaking through the event horizon and riding the wormhole until they reached their destination. The jumper emerged from the 'gate on the other side and into deep space just outside the orbit of a planet resembling Earth. At least it appeared to have similar amounts of landmass and ocean, plus distinct polar caps that made him suddenly recall the day in Antarctica when he'd first found out about the expedition, so many years ago now.

'Okay, Rodney. Do your scanning and let's find out if there's anything down there worth our time and energy,' Sheppard called back to him.

'Already on it,' Rodney replied, his tablet now fired up and running a sensor program. Sheppard took the jumper in closer to the planet and swept the surface as they orbited, waiting for Rodney to go off like some kind of alarm with highlights of the data he was receiving.

Unfortunately, it soon became evident McKay's enthusiasm was far from bubbling over. 'I'm not picking up anything of any value. There are some constructions, but no life signs. And no power signatures whatsoever. Looks like this place is a complete waste of time.'

Sheppard sighed, though he was somewhat relieved he didn't have to get out and trek around in rough terrain and changeable. Though he was feeling livelier already, he wasn't in the mood to listen to one of McKay's incessant grumbles about rain and treacherous terrain. 'I'll make another pass to be sure we didn't miss anything, but if there's still nothing showing up we'll head back and you can spend some time fixing those systems you were talking about earlier.'

He heard McKay give a small huff in return, but then nothing more, so assumed he was continuing to study the data the scans were feeding back to him.

'Anything?' Teyla asked the scientist hopefully, raising her eyebrows.

'Nope...nada, zip and zero,' Rodney sighed, throwing himself back in his seat. 'Not even a glimmer of a power signature for us to track. This trip was a complete bust. I told you we should let someone else do this stuff.'

'All right, Rodney. Let's not get mad about this. We knew there was a good chance we wouldn't find anything before we set off, but we had to check things to know for definite,' Sheppard reminded him, turning the jumper round and heading back toward the 'gate.

'Which is exactly why I should be back on Atlantis doing something more useful,' McKay snapped, annoyed by the lack of any significant data. 'Anyone can chase rainbows, but not just anyone can get Atlantis back to its former glory.'

'Sheppard said you could stay behind,' Ronon rumbled by way of a reminder of their earlier conversation.

Sheppard noted the slight hesitation before Rodney pulled together his answer. McKay was evidently having difficulty dealing with the part he'd played in Elizabeth's loss, and his inability to express himself was leaving him increasingly frustrated and edgy...more so than usual, though if anyone had asked him before all this had happened, Sheppard would have told them that wasn't possible.

'Yes, but like I said, if you people are out here, my place is with you. We're a team, right?'

'Rodney, we are not going to die the minute you let us out of your sight, so get past it!' Sheppard snapped. Then he regretted his outburst. It wasn't fair to drag McKay's true feelings into the light like that when he was already feeling so bad, and he wished he could take it back.

The silence his comment met with told him just how embarrassed Rodney was by his revelation. McKay wasn't always good at reading other people, and he clearly hadn't thought he was being so obvious in his paranoia. 'I...I wasn't thinking that at all,' he stammered, but the quake in his voice told Sheppard he was almost choking on the denial. 'I just don't see why you guys should get all the fun while I stay behind on Atlantis and work.'

'Well, we aren't smart enough to help you,' Ronon quipped, deadpan.

The colonel felt Teyla's eyes drilling into him, but he refused to meet her gaze. He knew she was angry with him for what he'd said to Rodney, that she thought he'd been insensitive raking up the scientist's raw emotions in front of all of them. Unlike McKay, Sheppard was uncannily good at reading others – no verbal confirmation of his suspicions was required – and normally he was more tactful than to broadcast them to anyone who was listening.

'Well, I guess I was mistaken,' Sheppard said more softly. 'Look, just sit the next trip out, Rodney. I'm sure there are more essential things you can be working on back at At –'

A communication from Atlantis interrupted him before he could finish his sentence. 'Colonel Sheppard, this is Atlantis. Please respond.'

'Copy that, Atlantis. This is, Sheppard. What's the problem?'

'The away team sent to M3P 147 made a significant discovery on the planet. They're on their way back to Atlantis now, and we thought you'd want to be here to meet them,' he heard Chuck respond.

Interest piqued, he demanded more information. 'What did they find? Please tell me it's a ZPM?'

There was a pause before Chuck's voice broke through again. 'No, Sir. It's something far more significant than that. They've found Dr Weir.'


	4. Chapter 4

The others had no hope of keeping up with Sheppard once he'd bounded out of the jumper. Teyla ran at full pelt through the corridors from the jumper bay to the Gate room, and though she and Ronon were by no means slow, neither of them could match the colonel's pace. Rodney, of course, was left panting along far behind them. Over the years of fieldwork, his fitness had improved a little, but he was still far more comfortable when sitting at a computer with a sandwich than moving at speed.

When she reached the control room, Teyla found Sheppard already demanding all the information Chuck had on the situation regarding Elizabeth's discovery.

'...and they were considering returning for reinforcements when Zelenka ran a bio signs scan and it came up with a life sign in the exact same spot as the replicator energy signature. When he double-checked, he realised the energy signatures of the nanites he'd detected identically matched the functions of those Dr McKay reactivated in Dr Weir, so they landed to check it out.'

Chuck glanced anxiously across at the rest of them, just as Rodney panted his way up to the steps to the platform where they had gathered for the update. Teyla could see a mixture of excitement and fear in Chuck's dark eyes. Clearly, he understood Elizabeth's discovery was not something to be celebrated unconditionally just yet. Teyla hoped Sheppard could be as detached in his thinking as he was. The colonel's sense of failure had been almost tangible since landing them safely on M35-117 without her, and she feared he would be so overwhelmed by relief to have Elizabeth back among them it might blind him to any potential threat she posed. She still had the nanites inside her, nothing had changed as far as they were concerned, so she still couldn't be fully integrated into life on Atlantis again.

'They know not to touch her, right?' Sheppard asked, his brow furrowed as he stared down into the gate room. 'We don't want anyone else becoming infected with her nanites until before we've ascertained they're still benign.'

'I told you, I programmed them so they couldn't communicate with the other replicators,' Rodney panted, pressing the stitch in his side in an attempt to diminish the pain.

'That was before she fell into enemy hands, McKay. She's been missing for three days; who knows what they did to her in that time,' Sheppard pointed out.

Teyla was happy to hear the colonel voice his scepticism so early in the proceedings. She hoped beyond hope that Elizabeth had been unaffected by the Asurans, but she couldn't shake the feeling they had found her far too easily. Why would the Asurans simply rid themselves of such an advantage after just a few days? Elizabeth had been the hub of life on Atlantis; nothing significant happened there without her approval. Perhaps the Asurans had simply raided her brain for the knowledge she possessed and then tossed her aside like a broken storage vessel. She couldn't believe they would do that, though. The part Elizabeth had played in Atlantis' escape would have angered Oberoth; surely he would have wanted revenge for such an act of treachery.

'Dr Zelenka has ensured everyone aboard the jumper knows the risks, and I've reminded everyone here. The team kitted up in hazmat suits to restrain her, and they're bringing her back to put her into the isolation room under Dr Keller's care.'

'Was she fully compliant?'

'I believe so, Colonel.'

Sheppard turned to look at them all now, and Teyla saw the doubt marring his expression. Though it was painful for her to see him so worried, she was glad he wasn't allowing his broiling emotions to override his common sense. She wanted to reach out to him, to tell him she understood how he felt and would listen if he needed to talk about it, but had no doubt he would reject the offer. Sheppard did not open up – that was just one of the many complex aspects of his personality, and the thing that made him most vulnerable in her eyes.

The 'gate activated, and Sheppard turned to the technician for verification of what was happening.

'We're receiving Dr Zelenka's IDC,' Chuck told them, and once again Sheppard was running.

'Drop the shield,' he yelled as he descended the stairs two at a time.

Teyla tried to follow him, but Ronon gently caught her wrist and stopped her. 'Leave him. He needs to do this.'

Though she wanted to pull free, she nodded and walked with him to the balcony overlooking the gate room. Sheppard stood to one side as the jumper swept in and landed, hesitantly approaching it as the rear hatch lowered. He remained in sight for a moment or two longer, his face scored with worry, then she saw him draw his sidearm and disappear inside the vessel.

Teyla glanced at Ronon and Rodney, seeing her own concerns reflected in their expressions. Though she wished they could give Elizabeth the rapturous welcome she undoubtedly deserved, she was glad the reception was going to be more tempered. She felt certain Dr Weir would understand their caution when dealing with her, after all, she herself had said they shouldn't have used the nanites to save her because it put Atlantis and its personnel at risk. Although angry at herself for even thinking such a thing, Teyla couldn't help but wish Rodney had just let Elizabeth's spirit go free when her body was failing. It had been her time; even now, she wasn't alive in the true sense of the word. Only those tiny machines stood between her and the afterlife. The Athosian couldn't imagine how she would feel knowing something so destructive lurking within her was the difference between survival and death.

After a few moments of inactivity, she saw the jumper team emerge first, each of them still wearing their protective suits and with their P90s poised ready for action. Next came Zelenka, studying his tablet as if his life depended on it as he picked his way down the ramp and across the floor. And finally, Dr Weir appeared walking slowly with Sheppard, who held his gun trained on her and kept a distance of just a little more than an arm's length between them. Looking shaken and fragile, Elizabeth cast her eyes around the gate room, looking tearful as she drank it all in. Teyla supposed she had never imagined to see the place again, and felt her own eyes fill with tears at the thought of how overwhelming being among friends again would be for her.

Sheppard activated his earpiece, and, listening carefully, Teyla could just about make out his instruction to Chuck. 'Have Dr Keller suit up and meet us in the isolation room. Make sure our route is clear.'

'Yes, Colonel,' Chuck replied, and was straight onto it.

'I'm gonna go talk to Zelenka and see what's going on,' Rodney mumbled, shuffling away with his head bowed as if looking at Elizabeth was too difficult for him.

Teyla considered following him, torn between wanting to support John and wanting to help Rodney, too. Both men needed support though neither would admit it, and attempting to ease the burden of guilt they both carried had been emotionally exhausting for her. Judging Rodney would probably prefer to be left to his work, she decided to keep an eye on John instead.

'We should go to the observation gallery and wait for Colonel Sheppard to join us there,' she suggested to the Satedan standing beside her.

The giant man looked down at her and shrugged his broad shoulders. 'Not sure I'll be much use,' he grunted.

'Just being there will help,' she assured him, giving his forearm a squeeze. 'I expect both Rodney and Colonel Sheppard will find this a trying time. We must show a united front to let them know we are behind any decisions they make.'

'What if they decide on different things, like McKay did when he reactivated those nanites?'

Teyla looked down into the gate room to where Elizabeth still stood beside Sheppard, awaiting her transfer to the isolation room. Even from that distance Teyla could tell she was trembling. She had never imagined she would see a woman like Dr Weir reduced to this. Sheppard obviously saw it, too. He spoke to Elizabeth now, and although his voice was too soft for Teyla to hear the actual words, she could tell from the pitch and the way he lowered his gun just a little that he was doing his best to reassure her. In response, Elizabeth nodded quickly, clearly biting back tears as she averted her eyes to the polished floor rather than face him. To Teyla, it looked as though Elizabeth felt ashamed somehow of what she had become.

Sheppard looked up to the balcony and met Teyla's gaze, giving her a brief and somewhat sharp nod before ordering the team to move out. The pilot took the jumper up towards the bay as Radek and Rodney, who had now joined him, lead the way out of the gate room, leaving Sheppard to bring up the rear.

Once they were all gone, Teyla spoke to Ronon again. 'Come, we must see what we can learn about Dr Weir. I wish to know just how she came to be on that planet.'

'Yeah, I'm wondering about that, too,' Ronon admitted, and they headed to the gallery in the hope of finding their answers.

*****

Elizabeth looked frailer still once dressed in infirmary scrubs and sitting on the raised bed of the isolation room. Several hazmat suited members of the medical staff tested her vital signs, took blood samples, and scanned her while she sat on the bed, her legs dangling a few feet above the floor and making her look like a lost and frightened child rather than a former commander of the city.

Teyla's heart ached for the woman she considered a good friend as well as a colleague. The one thing she needed – reassurance that everything was going to be fine, and that she had come to no harm – was the one thing no one was willing or able to give her. The Replicators were so much more advanced than they were, there was no way of telling what they could have done while leaving no sign of their deception. She suspected only time would tell – that and the continuous testing that would take up most of that time.

A few moments later, Sheppard joined both she and Ronon in the gallery above the isolation room, looking down on the one time leader of Atlantis.

'How is she?' Teyla asked him, more as a way of starting a conversation than needing the information. She had seen for herself how Elizabeth was coping, and the rest was yet to be ascertained.

'Scared,' Sheppard replied without looking at her, 'but physically she appears to be in good shape.'

Teyla couldn't help but mark the way he said 'appears', as if he didn't trust what his eyes were telling him. She understood his reticence, but could also see how much it hurt him to feel that way. His body language was tight and restricted, as if he was reining in the desire to lash out to vent his frustration. But she had come to understand that was how John Sheppard dealt with things. He bottled them up until he found ways to cope without facing them, each time leaving another deep scar etched in his psyche.

'What about the readings Rodney and Radek have been analysing?' she asked.

'So far, there's nothing out of the ordinary. The nanites are behaving in exactly the way McKay programmed them to, so no sign any capacity to communicate at the subspace level or to function at any other level than to preserve her life...which means they pose absolutely no threat to us.'

'But you are still worried,' she pushed, watching his reactions.

He grimaced, rubbing his chin as he contemplated his answer. 'I don't understand why they would have dumped her they way they did. I just need more answers before I'm comfortable with this.'

'That is understandable...and I'm sure Elizabeth also recognises that fact,' Teyla soothed. His hand was beside hers on the rail, and she felt the urge to lay hers on his as a gesture of support and comfort. She refrained from doing it, though, knowing it would only add to his apparent discomfort.

'Maybe they just didn't think we would find her,' Ronon suggested. 'The Pegasus galaxy is a big place – what were the chances they'd dump her on a planet so close to where we ended up landing?'

Teyla watched John's reaction to that, his profile highlighted by the light from the isolation room. His expression remained rigid, unchanging, but she could see his tension as the muscles of his jaw pulsed with the pressure of his gritted teeth. Evidently that was the problem; he obviously thought the chances of that were low, and yet it had still happened. She sensed he wanted to go to Elizabeth, to make the others stop poking and prodding at her and give her some space and time, but also understood there were protocols to follow and he had to let everyone do their jobs. Teyla, too, felt an almost overwhelming desire to rush to Elizabeth and embrace her friend to welcome her back to Atlantis, but shared his caution. The woman in the room beneath them, the one who looked like their friend and leader, was harbouring the most dangerous life form known to them in this galaxy, and as such, they had to keep their distance.

'How long before Dr Weir will be allowed to move freely again?' she asked, again watching for his non-verbal responses as closely as she listened to his actual words. It was a vital skill when trying to measure how Sheppard felt about things, and one she'd honed over their time working together. Though he was a man of few words, he expressed himself so clearly through expressions, gestures and his posture that she almost always knew how he felt.

He remained stiff and unmoving, his behaviour telling her he was barely controlling his anger at the situation they all found themselves in. 'I don't know, but I suspect it could be days at the very least. The Asurans are smart and patient; if this is a trap, they won't mind waiting a while to catch us out.'

_A trap. _Now Sheppard had voiced that thought she realised that was how she felt about it, too. The Asurans had given them back the one person they had managed to capture, and the fact Elizabeth had been found on a planet in the area of the galaxy they had moved the city to meant there was a chance they had at least some idea where they had escaped to. But then she doubted her own instincts. The Asurans were powerful, and they had seriously damaged the city in both their initial attack and by forcing them to flee Lantea. If they knew where they were, she felt sure they would have continued their assault and finished the job by now.

'So what happens now?' Ronon asked from beside her.

Sheppard sighed and pulled himself up straight. 'Now, I have to contact the SGC and let them know what's happened. I'm pretty sure they'll have their own ideas about how we should deal with all this.' After one final glance in Elizabeth's direction Sheppard walked away, his shoulders hunched and legs leaden, as if he literally carried the weight of the world on them.

Teyla watched him go, then felt Ronon's hand on her shoulder. 'I wouldn't want to be in his shoes right now. I think we should give him some space to work out how he's going to deal with all this.'

'I agree,' Teyla nodded, reaching up and squeezing Ronon's hand. 'Perhaps we should retrieve Dr Weir's possessions from storage and take them to her personal quarters. Hopefully, we will be able to return them to her soon.'

'Hope so,' Ronon replied, giving her a warm, encouraging smile.

But even as they headed to the storeroom, Teyla felt in her heart that none of those items would never make it back to Elizabeth's office. The nanites keeping her alive meant life had permanently changed for Dr Weir. She doubted the SGC or the IOA would ever trust her to command Atlantis again. What Teyla hoped for most now was that she and her teammates would be able to see past the nanites and find a way to trust their friend again, whatever the IOA decided to do with her.


	5. Chapter 5

"_With you I will be quite frank," said Anna Mikhaylovna. "There are not many left of us old friends! That's why I so value your friendship."_

_Anna Mikhaylovna looked at Vera and paused. The countess pressed her friend's hand._

"_Vera," she said to her eldest daughter who was evidently not a favourite, "how is it you have so little tact? Don't you see you are not wanted here? Go to the other girls, or..."_

_The handsome Vera smiled contemptuously but did not seem at all hurt._

Sheppard sighed, laying _War and Peace _face down on the bed beside him still open at the page he was reading. He'd read that handful of paragraphs several time and they just weren't sinking in. The main reason for that was he didn't want to be in his room reading; he wanted to be in his office keeping an eye on Elizabeth. The techs had set up a screen in there so images of her treatment and confinement could be relayed straight to him when he wanted to know what was happening. Keller hadn't been too happy with a non-medical person observing her patient so closely, claiming it was a breach of Elizabeth's human rights. But then, when Sheppard had pointed out the nanites were threat to every person on the base and were therefore also a military issue, not just a medical one, she'd been forced to back down. Keller had disobeyed his orders once, he'd be damned if he'd let her do that again.

So, he'd spent the past several hours in his office – Elizabeth's office – monitoring the situation, until Dr Keller had arrived to give him an update and, noticing how tired he looked, had insisted that he go to his room and get some rest. Though he'd felt like disagreeing just to prove who was in charge, he'd realised that was childish and detrimental to his own well-being and so had consented.

Now, constantly distracted by what might have happened to Elizabeth, he regretted giving in to her. Though he didn't want to, he kept remembering what it felt like to have his mind probed by the Replicators, the sensation of hot pokers sliding in and out of his brain, the abuse of his thoughts and memories – the destruction they made him imagine was real. Had Elizabeth been put through that time and again, and if so what damage had it done to her? It was giving him a headache just thinking about it.

Much as he knew he couldn't physically do anything to help, he couldn't shake the feeling his place was overseeing their 'patient'. Although he was only temporarily in charge, at this moment all the people inside this city came under his care. It was common sense that he should keep an eye on things until they were certain Elizabeth was okay, yet, at the same time, he also knew he desperately needed sleep to be able to perform his leadership duties effectively. Much as it galled him to admit it, he knew Keller was right to suggest he should leave it to the medical team to monitor her for the night. The sooner he got some sleep, the sooner he could get back to work in the morning.

Punching his pillows flat, he lay back and closed his eyes in an attempt to get some much-needed rest. With Elizabeth back among them he knew he should be able to relax a little, but something still felt off about the situation, something he couldn't quite put his finger on. Part of him had wanted to question her straight away, to understand as much as he could of what she'd been through not just to assess the threat she posed, but also, at some level, to confirm his mistrust was justified. However, another part of him had willingly accepted Keller's observation that she needed to recuperate before she would allow Elizabeth to face such a stressful situation. Though it postponed his understanding of the nature of her imprisonment, he figured since the situation appeared to be contained, he could wait a little longer.

The image of her huddled in the back of the jumper, her hands bound tightly in front of her, while everyone kept a safe distance away popped into his head, bringing with it a wave of pity and disgust; pity for her, and disgust that the Asurans had reduced them to the need to cuff her like a criminal. She didn't deserve this treatment; at least he didn't think she did. He'd sensed no malice or deception on her part, merely relief tempered with fear. He tried to imagine how she would feel knowing she could never be allowed to retake the position she'd once held on Atlantis. If someone told him he could no longer be part of Atlantis he would feel like his world had ended, and he guessed that was pretty much how she felt, too. Elizabeth was a strong leader, and even though they'd clashed sometimes, he'd always admired her. She would be a hard act to follow; there could be no doubting that.

He opened his eyes and looked around his room for something else to distract him from his worries. His eyes roamed over the photo of Eval Kneval on his nightstand, his skateboard, and then around the walls until they fell on his surfboard propped in the corner. What he wouldn't give to find a nice quiet beach where he could catch a few waves right now. Surfing always helped him clear his mind and relax, but since the city was in such a dire state, he couldn't just grab up his board and go pull a few cutbacks. Besides, there might yet be some unknown carnivorous beasts lurking near the shores of M35-177; they hadn't had time to find out. There weren't many things he missed about Earth, but knowing where it was safe to practice his favourite hobby was a bonus this planet couldn't provide him with...at least not yet.

Realising he wasn't going to get to sleep any time soon, Sheppard decided to go back to his office and watch the proceedings with Elizabeth a while longer, at least until exhaustion finally knocked him out, which he figured it had to do eventually.

He reached his door and activated it just as Teyla was about to announce her arrival on the other side. 'Oh, Teyla...I was just on my way out.'

Teyla looked just as shocked as he was on finding her there. 'John...I thought you had retired to your quarters for the evening.'

'Well...I had,' he said sheepishly, scratching his unruly hair. 'But since I can't sleep yet I thought I'd go check on Elizabeth again.'

'No need. I was just in the infirmary and Dr Keller assures me she is doing well and there are still no signs of any problems with the nanites. She also said I was to make sure you got some food and some rest, as she suspected you might try to return to work. So...' She lifted the tray she carried, offering it to him while still strategically blocking his exit route.

'Oh...thanks,' he muttered, taking it from her and stepping away from the door.

'It's lasagne,' she said as he turned his back. 'I know you like Italian food. Oh, and there's salad and orange juice because Dr Keller said you needed good food to keep up your energy levels.'

Sheppard suspected she was trying to keep the conversation open, and peered back over his shoulder at her. 'Smells good. Thanks.'

'Would it be all right if I joined you for a while,' she asked, raising her eyebrows in an expression caught somewhere between sympathy and hope.

Although his heart sank at the thought of one of Teyla's cunningly probing conversations, he nodded and gestured for her to come inside. She stepped into his room and allowed the door to slide shut behind her as Sheppard sat down on the bed and took the lid off his meal. It looked like a double serving, probably because Teyla knew he'd skipped lunch. She noticed things like that. 'What's in the flask?' he asked, noticing a metal container beside his bottle of orange juice.

'Hot milk to help you sleep later,' Teyla said, edging her way across to him, her fingers knitted together as she twisted her hands awkwardly in front of her. Sheppard sensed she had something specific she wanted to talk about and so invited her to sit. She perched on the end of his bed, leaving him plenty of room to manoeuvre as he ate.

'You must be overjoyed to have Elizabeth back among us,' she ventured, as he swallowed his first mouthful of lasagne.

Not looking at her, he loaded up his fork with more food. 'Well, it's certainly unexpected...'

'But you do not know whether to be happy or not?'

He chewed his food with the growing realisation he wasn't going to get away with ducking her questions. Teyla wanted to know how he was feeling, something he was never very comfortable with revealing, but that she had an uncanny knack for wheedling out of him regardless. 'It's early days, Teyla. We still don't even know if the repairs the nanites put in place will hold, let alone if anything worse has happened since then.'

He managed a few more mouthfuls while his friend pondered his response. 'Rodney believes the nanites continue to behave just as he intended them to. Are you worried they may malfunction?'

Pouring the contents of the juice bottle into the glass on his nightstand, Sheppard allowed himself to drink some before answering again. Teyla often pinned him down for these kinds of conversations at mealtimes, as if she thought the lure of food was too strong to stop him making an escape. But it was never the food keeping him there; he just didn't mind Teyla thinking that so went along with the charade.

'Elizabeth was in Asuran hands for any time up to three days. I think it would be pretty foolish not to feel cautious about how that time might have affected her.'

'You do not trust her?' Teyla asked, her eyes widening just a fraction.

'Oh, I trust Elizabeth...but I sure as hell don't trust the Replicators. I don't know...it's just that finding her so soon seems too...convenient.'

Teyla nodded while he ate some more. He'd been so wrapped up in dealing with the latest developments he hadn't realised how hungry he was until he'd started eating. His stomach ached at the introduction of the food, and he suspected he would need more than just hot milk to settle it enough to get him a good night's sleep. He could always slip out for more food if necessary. He was the leader of Atlantis, after all; they couldn't actually confine him to quarters.

The Athosian remained quiet for a moment or two longer before asking, 'Do you believe she has been sent here to entrap us in some way?'

Sheppard shrugged as he chewed thoughtfully, not really understanding what his feelings toward Elizabeth were right now. He was happy to have her back, yet, at the same time, simply having her there put the entire city and its inhabitants at risk, whether she'd been tampered with or not. No matter how supremely confident McKay was that he had made sure the nanites couldn't communicate with the other Replicators, the science involved in them was so sophisticated there could be no way anyone could be one hundred percent certain things would stay that way, not even him. Replicators had a way of adapting to their circumstances, and if there was even just the tiniest error in Rodney's programming, they would eventually find it and take advantage of that. Once again, he found himself wishing Elizabeth had died in the initial attack by the Replicator satellite, although it seemed likely that would inevitably have led to all their deaths. He hated feeling that way about her, but those nanites complicated things in ways he wasn't sure they could ever get past. No matter which way he looked at it, he felt he'd lost something special with Elizabeth; a bond had broken down that could never be fully repaired...at least not while she had those damned nanites inside her.

'John, are you all right?'

Teyla's gentle voice tugged him out of his thoughts and back to the here and now. His fork was poised halfway to his mouth where it had stopped while he thought about her question, and all that Elizabeth's abduction by the enemy meant.

'Er...yeah...yeah. I'm good,' he replied, nodding emphatically as if that would convince her of his honesty.

'You didn't answer my question,' she pointed out.

He sighed, shovelling in the last mouthful of his meal as he set his tray aside.

'I know. I'm not deliberately avoiding it, it's just that I can't really say what I feel. I want to believe she's _our_ Elizabeth and she's come back to us, I want that more than anything in the world, but I don't want to get my hopes up in case...'

'...something goes wrong,' Teyla said flatly, finishing his sentence for him.

He noticed now that she looked a little crestfallen herself, something that was very unusual for her. Teyla was one of life's eternal optimists, much as he had been when he'd first arrived in the Pegasus Galaxy. Gradually, their fight with the Wraith and the loss of close friends and colleagues had dulled the shine for him, but Teyla had always come back just as strong as ever. He knew she'd taken the news of Elizabeth's 'death' badly; Ronon had told him he'd found Teyla crying over her belongings in her office and so had stayed to help to ease the burden she had taken upon herself. He, for one, had been very grateful she'd offered to clear Elizabeth's things, certain he couldn't have managed it himself.

'Are you okay, Teyla?' he asked. 'I didn't mean to worry you talking about all my doubts like that. I'm sure things'll work out.'

'Do not concern yourself,' she said, forcing on her customary smile. 'You have said nothing I didn't already suspect.'

He turned so he could face her a little more directly, hitching one leg up onto the mattress. 'Don't worry over this. Ronon's probably right; the Asurans just didn't see Elizabeth as worth their time and effort.'

This time when Teyla smiled at him, it was even more of a struggle for her. 'Well, let us hope Ronon is correct. Now, I will leave you to get some sleep. Be sure to drink that milk; it will help you to relax.'

She stood and collected up his meal things, heading for the door.

'Thanks for this, Teyla,' Sheppard called after her. 'You know...the meal and the talk.'

'You are always welcome, John,' she said, dipping her head respectfully as she left.

Looking at the flask on the nightstand then checking his watch, Sheppard decided to save the drink for later. Instead, he reached into his top drawer and pulled out a power bar from the supply he kept there in case he got a night time attack of the munchies. His fast metabolism often left him hungry after his evening meal, especially when he got stressed. The power bar seemed to top him up nicely, and then he stretched out on the bed, running over his chat with Teyla again.

Though it worried him that she, too, had doubts about the way Elizabeth had returned to them, it was also reassuring to know he wasn't the only one thinking it was all too easy. Not only had the Asurans released Elizabeth relatively unscathed, but they had also left her on a planet close enough to their new home for them to want to investigate it. That seemed like more than a mere coincidence to him, but he sorely hoped he was wrong. He really did want Elizabeth to be back for good.

He hadn't realised quite how close the two of them had grown until Dr Keller had told him the extent of her head injury. He'd found it hard to hold it together in front of the young doctor, and he didn't think he'd fooled her into thinking he wasn't as deeply affected as he really was for one minute. He'd almost cried in front of her, something he'd hardly done since he was a kid, although Carson's recent death had wrung a few reluctant tears from him, too. Way back when he was no more than six, when his horse had thrown him and he'd broken his arm, his dad had called him a wimp and told him only girls wailed the way he did, and he'd taken that message to heart.

But no matter how foolish he felt about reacting that way, he couldn't change the impact her loss had on him. He considered Elizabeth a good friend, one he even flirted with from time to time because he felt so comfortable with her, and that wasn't something he normally did with women he wasn't hitting on. Would he have cried if it had been Teyla, Rodney, or Ronon in that hospital bed that day? Damn right he would have, and every time he would have heard his father's voice picking at him, making him feel stupid and feeble just as he had through his childhood.

So, for the most part, he would continue to keep his feelings to himself. That was the legacy his father had given him; an ingrained belief that real men didn't let the pain show. He would grit his teeth and deal with Elizabeth in a professional way – no matter what the outcome or how troubled he was by the prospect of losing her again.


	6. Chapter 6

_Pain erupted through her head in an almost volcanic surge as Oberoth delved into her memories once again. Elizabeth blocked him as best she could, letting only tiny, ineffectual remembrances surface to appease or confuse him, depending on her mood. Right now she had pushed down her fear and was righteously pissed-off, and so threw him a particularly meatless bone of her falling off her bicycle as a child and scraping her knee. She was more than aware that the triviality of the material would infuriate him, but she didn't care. She knew she would not survive this imprisonment, and so was determined to take her memories of Atlantis and the people sheltered within its walls with her. Once Oberoth had tired of trying to attain information she would be killed or left to die alone in the cells, whichever satisfied his loathing of her most. Her fate was sealed whatever she did, so this was her last opportunity to do something for her friends – her final selfless act._

_She wondered if the nanites inside her had changed her somehow, because that thought wasn't nearly as frightening as she knew it should be. Somehow, the thought of dying and all this being over left her calm and serene, giving her the strength to hold out despite the pain._

_Oberoth withdrew his hand from her forehead and glared at her like a bad tempered Rottweiler. As the illusions he's fed her vaporised, she realised she was still in a cell just like the ones back on Atlantis, the thick bars and shielding impenetrable unless you knew the code to get out. 'You really should co-operate, Dr Weir,' Oberoth rumbled, his eyes narrowing to little more than burning slits in his broad and wrathful face. 'Tell us what we want to know about Atlantis, or we will torture you in ways you cannot even begin to imagine.'_

'_Your threats are pointless,' she spat back at him, raising her chin high. 'I've already sacrificed myself. I'm prepared to die for my people, so you can't do anything to me now that will make me talk.'_

'_We don't need you to talk, we only need you to stop blocking us. Those nanites you possess certainly make you strong, but they won't keep us out forever. Why not make the process easier on yourself and let us take what we need. We might even spare you – or perhaps build you a new body, one that will be far less fragile than the flesh and blood you are wrapped in now.'_

'_I don't think so,' she said, smiling fiercely at him. 'I'm happy with my body just the way it is, thank you, and considering you've made yourselves look like us, I think you're actually rather envious.'_

_Her confidence only added fuel to the already raging flames of his ire. 'It really would be better if you gave us the information we seek willingly, Dr Weir. We will be far more forgiving in our treatment of your friends if you assist us.'_

_A surge of panic lurched in her stomach at the mention of her friends back on Atlantis in his threats. But she didn't believe Oberoth would spare them any pain if she helped him; he was designed to be aggressive and he did it frighteningly well. 'You mean you'll kill them more quickly?' she asked. 'Well, I refuse to play any part in it. If I can hold the information from you, you'll never be able to find them anyway.'_

'_Of course, you are assuming Colonel Sheppard and Ronon Dex escaped...and I'm afraid that assumption is incorrect.'_

_She watched in horror as Sheppard and Ronon were dragged into the room outside the bars, struggling all the way against their impossibly strong captors. Neither man would submit to being forced to their knees, and when one of the replicator guards kicked the back of Sheppard's calf, Elizabeth was certain she heard more than just the sound of his boot hitting muscle. The throat-scraping scream forcing its way out through his clenched teeth as he buckled let her know she was right. Two Replicator guards held each man's arms pinning them firmly in their kneeling position. Ronon fought fiercely and almost mustered enough strength from his seeing his friend's pain to throw his oppressors clear, but when two more joined in the battle, he was quickly overcome._

_Oberoth led Elizabeth out of the cell to make sure her view of the men was unimpeded. His grip on her arm made her wince, and the thought of how much worse the pain of John's injury would be sent her stomach into a spasm of somersaults._

'_You see, your sacrifice wasn't completely successful, Dr Weir,' Oberoth stated, a faint smile curling his lips. 'Dr McKay was able to escape us with the ZPM you'd stolen, but these two were just a little too slow to make it back to their vessel. Now, do you really think you are strong enough to withhold information while your colleagues are tortured before your very eyes?'_

_She opened her mouth, but no words were forthcoming. She looked toward Sheppard, a cold sweat breaking out on his ashen face, and knew he was already in more pain than she wanted to think about. Oberoth was right; she wouldn't be able to keep the information he sought from him._

'_Don't tell him anything,' she heard Sheppard rasp, his two captors either side of him twisting his arms awkwardly behind him._

_That helped to steel her nerve, and she set her jaw, glaring back at the furious face of the psychotic Replicator. 'I won't tell you where they were heading. You can't make me forfeit the lives of everyone on the expedition to ease our passage.'_

'_Yeah...do your worst,' Ronon growled, his teeth bared like an angry dog preparing to fight._

_Oberoth held his hand out before him, the nanite cells melting and morphing until they formed an alarmingly sharp and reflective blade._

'_We'll, let's see if you feel so brave when I've cut out your tongue, Ronon Dex,' he charged, moving toward him._

_Then, he stopped. A moment of stillness followed as Ronon continued to glower, but that the Replicator slowly turned toward Sheppard. The colonel seemed to sense the change in his intentions, and lifted his sagging head to look at him._

'_I believe I will let Ronon Dex continue to rave since you are more important to Dr Weir, Colonel Sheppard.'_

_Elizabeth felt a prick of embarrassment, cursing herself for such a futile emotion. They were all about to die; it didn't matter if Sheppard learned the truth now. Oberoth put the blade under Sheppard's chin, lifting his head higher and slicing the outer layers of his skin in the process. A trickle of blood ran the length of the smooth blade, soaking into the simulated material of his sleeve. 'You appear so strong, and yet your bodies are so feeble and slow to mend.'_

'_Screw you,' Sheppard spat back, flinching as the blade cut just a little deeper._

_Oberoth smirked at the colonel's feeble attempt at defiance. Elizabeth swallowed, her arid throat almost sticking shut in the process. She'd been in the position of withholding information as Sheppard was tortured once before; she didn't think she had the strength to hold out again, not with him right here in front of her. 'Please stop,' she heard herself whisper, without even consciously forming the thought._

'_With pleasure...as soon as you give me the location of Atlantis.'_

_She looked to Sheppard again, his green eyes meeting hers and demanding that she not to speak. But she could see his agony and it tore into her soul. She couldn't be the co-perpetrator of his torment again._

'_They –'_

'_Elizabeth...don't' _

_The colonel's firm instruction gave her strength once more. She clamped her mouth shut._

'_Very well,' Oberoth said flatly, slicing into the biceps of Sheppard's left arm._

_He groaned through his still clenched teeth, but refused to let out another scream. _

_The Replicator struck again and sliced across his left arm, then nodded to a guard who stepped forward and pushed his boot into Sheppard's back, forcing him forward as the others held onto his wrists. The additional pressure on his wounds opened them up, and Elizabeth could soon see a slick darkness oozing through the fabric of his shirtsleeves._

_As if sensing her resolve wavering, Oberoth cut the colonel again across his exposed forearms, where the blood could run freely and drip to the polished floor. The guard behind pushed even harder, the strain making the blood flow increase._

'_Stop this!' Elizabeth cried, desperately trying to think of some way of assuaging Oberoth's desire for revenge without anyone having to die. 'Stop, please. There has to be some way we can come to an agreement. We could fight the Wraith together...there really is no need for us to be enemies.'_

'_You tried to destroy our planet, Dr Weir. Hardly something that demonstrates a willingness to form a friendship.'_

_She'd known that act of aggression would come back to bite them, but no one had been willing to listen. Now they would pay the penalty._

_Oberoth sliced again, this time into the colonel's shoulders. He shuddered against the pain and ground out a groan that told her how much this hurt him._

'_Do something!' Ronon growled at her, pulling hard against those restraining him, so hard he actually momentarily unbalanced them. They soon re-established their footing._

'_Don't listen to him,' Sheppard panted, rivulets of perspiration now running down his face. 'Think of Atlantis.' The foot in his back pressed harder and he whimpered despite his best efforts not to._

_She did what he asked. She thought of the people she knew there, of all the lives depending on her silence, then Ronon shouted, 'They're killing him!' and shattered those images out of existence. All she could see was the suffering of the man in front of her...and it was all down to her._

'_Enough.' The guard stepped back and Sheppard immediately looked more comfortable despite his obvious injuries. Oberoth walked toward Elizabeth and she let out the breath she'd been holding, thinking it was over at last. 'You clearly have no intention of telling us what we wish to know. It's time to finish this.'_

_Without warning, he extended his arm sharply in Sheppard's direction, the nanites reforming into a lancing spear that penetrated just beneath Sheppard's breastbone and exited through his back, spreading out into a grappling hook shape which he used to drag the shocked and failing colonel toward him. Sheppard's body fell limp, only Oberoth's mutated limb stopping him from collapsing._

_Elizabeth wanted to scream, but nothing would come. She watched as Sheppard's eyes glazed before her, the last embers of his life extinguished by her refusal to comply. She had brought him to this by her supposed act of selflessness. Then she saw it, a flicker in the image, a fault, and suddenly the coding generating the whole illusion became clear to her. John, Ronon, the guards, everything except Oberoth was a Replicator generated image, and with that realisation, the scene broke down into its separate pixels and fell away from around them._

_Though still shocked, the fact he had needed to fake that scene told Elizabeth what she desperately wanted to know. The rest of her team had escaped; John was safe._

'_Seems I'm not as easy to fool as you thought,' she announced, her tone sounding far more confident than she actually felt. 'I won't tell you where they are, Oberoth – not ever.'_

_Unexpectedly, the Replicator's face cracked into an unnerving smile, then he gave a full, throaty laugh. 'You are but one, Dr Weir, and we are many. You have no hope of succeeding.'_

_Annoyed by his continued air of superiority even in the face of this defeat, Elizabeth just folded her arms across her chest and said, 'We'll see.'_

Elizabeth's eyes opened to the lined, graphite grey walls of the isolation room. The clash with Oberoth had been nothing more than a nightmare replay of her imprisonment, and relief flushed the adrenalin from her veins and helped her to relax as she remembered she was now safe and among friends. She had never imagined she would see Atlantis again when the Asurans had abandoned her on the uninhabited planet Radek had found her on. After two days of isolation and barely surviving the arid landscape and the freezing night time temperatures, she'd come to terms with the fact she would die alone there. But then the jumper had come and things had changed.

She'd considered hiding at first. She didn't know if it was the jumper Oberoth's soldiers had dropped her off in or one of Atlantis' own, but either way she felt the best thing would be if she concealed herself from whoever had come and just died there. Even with the nanites desperately fighting to keep her alive, there was only so long her organic components would last without food and water. But she'd realised how pointless concealing herself would be. Whoever they were, and whichever side they were on, they each had ways of tracking her that were beyond her control. So she'd held her ground and hoped for the best.

It was with a small amount of relief she first spotted the hazmat suits. It was her own people, not Oberoth back to see if two days on the planet had weakened her resolve. The military team had obviously come looking for her, as there was no sign of surprise in their expressions when they found her, merely concern for her wellbeing, and perhaps for themselves, too. It was good to see Radek among them; another civilian with her made her feel less intimidated by the P-90s the marines held trained on her. Still, it came as a great relief to know that Atlantis had survived the flight through hyperspace and landed safely with no further loss of life. She might not be in control of the place anymore, but that didn't mean she cared any less about it or its inhabitants. Yet, much as she was glad they'd come to rescue her and she could now return to what she considered her home, some deep-rooted fearful corner of her subconscious knew it would have been better all round if they had never found her.

She couldn't help but smile now as she recalled the elation she'd felt in discovering the ZPM she'd helped secure had saved Atlantis. It felt wonderful to know her friends and colleagues were still alive, and even with all the restrictions she faced due to her condition, she felt safer now than she had in days. But there was one person she really wanted to talk to, the first person who had rushed to the jumper as it had come to rest in the gate room.

John.

She'd still been in shock as he'd come into view in the jumper; John Sheppard, now Leader of Atlantis, uncomfortable with power, but taking up the reins as was expected of him none-the-less. It was just like him to be the first one in there rather than delegate the responsibility to someone else. The man was his own worst enemy, never cutting himself any slack or taking the easy option. Poor John. Having command of the military aspects of Atlantis didn't faze him – that was his comfort zone – but she knew having overall command was something he'd never wanted, though he'd never voiced that fact out loud. Not once in their years of working together had she sensed any desire in him to usurp her position. He was her friend, and she suspected all the added pressure of losing and then finding her again on top of everything else he'd taken on board had pushed him hard. But he would cope...he always did. That was what John Sheppard was all about. When everyone else around was losing their heads, Sheppard could be counted upon to think of or do something to save the day.

She looked up to the observation window hoping to see him there, but no one was watching her. She sighed, wondering how long it would be before anyone joined her.

As if in answer to her unspoken question, the door to her room opened. Dr Keller, complete with orange hazmat suit, entered with a tray bearing breakfast for her.

'Good morning, Elizabeth,' Keller chimed from behind her visor, giving her a warm smile. 'How're you feeling today?'

'Good,' Elizabeth said, although she sounded a little uncertain, even to herself. 'Is that for me?'

'Well, I wouldn't be so cruel as to bring my own breakfast in here and eat it in front of you,' the doctor chuckled. 'There's some toast and yoghurt, and a strong cup of coffee for you. Teyla told me that's how you like to start the day.'

'Wonderful. Just what I need.'

'Is it okay if I just run a few routine tests and scans before you begin?' Keller asked apologetically.

'Of course. Do whatever you need to do.'

Keller set the tray aside on the table beside the bed so she could begin her work. 'Okay. Could you lie down for me so I can get a clear picture from the scanner?'

Elizabeth lay out straight and Keller passed a portable scanner over her, taking readings she could examine later. Then, she took her temperature and blood pressure, and finally another small vial of her blood. 'I'm sure you'll be relieved when we can stop poking you full of holes,' the doctor joked, giving her another of her broad smiles. 'I'll try to make sure we don't turn you into a sieve before then.'

'Well, whatever you do, it won't be as bad as what the Asurans did to me,' she assured the young medic, sitting up again.

Keller's smile faltered at that, and she looked as if she didn't quite know how to respond. 'Er, yeah. I imagine not. I've got a feeling a few people might want to ask you some questions about that later if you're feeling up to it.'

'I wouldn't expect anything less,' Elizabeth smirked, reaching for a piece of toast from the tray Keller had now placed beside her. 'Has Colonel Sheppard been to check up on me today?'

The way Dr Keller's eyes flicked briefly up to the camera in the corner of the room told her John would already be aware of her question. She wasn't surprised; if the roles were reversed she would be keeping an eye on him, too. She wondered if he'd been watching her since she'd woken, then realised he probably had, and more than likely for a while before that if she knew him as well as she thought she did.

'Er, I don't think I've seen him this morning. Is there any particular reason you want to see him?' Keller asked.

'There are some things he and I should talk about, that's all...in private.'

'Oh,' Keller said, again glancing toward the camera and looking a little awkward.

Elizabeth realised the doctor had misinterpreted her meaning. 'Oh, no. When I say in private I'm not suggesting it's anything...you know...intimate. It's just that the colonel doesn't really like to talk openly, and I need him to understand he's in no way to blame for what happened to me.'

'Oh, I see,' Keller giggled. 'Sorry. Well, I'll go see if I can find him and let him know you want a chat. I'll make sure you get some privacy.'

'Thank you, Jennifer,' Elizabeth called after her as she left.

The doctor gave her one last smile and departed, leaving her to enjoy her breakfast in solitude.

oooOOOooo

Sheppard heard Keller approaching the office, but didn't turn to acknowledge her, preferring to keep up his watch over Elizabeth via the image relay. She ate quickly, and he found himself wondering if the nanites affected her appetite along with everything else they were doing to help her ailing body. He hated the fact he was looking for trivial differences like that. They weren't important changes, but made him feel just a little more comfortable around her.

'She's one strong woman,' he heard the doctor sigh as she sat down opposite him.

'Yes, she is,' he agreed.

'I take it you heard what she said?'

He nodded.

'So you'll go and talk to her?'

'Yeah...later. I have a few other things I have to do first.'

He knew she was nodding without looking at her, but he could also tell she had more she wanted to say. He waited for her to continue.

'Did you get some sleep last night, Colonel?' Keller asked.

He glanced at her before returning his attention to the screen. 'Some.'

'You still look tired.'

Sheppard didn't want to go into detail about the kind of night he'd had. Though, when he pieced it all together, he had probably managed a total of four hours, his sleep had been so regularly interrupted by Replicator fuelled nightmares that he doubted he'd managed to get any real rest at all. Three strong cups of coffee swiftly thrown back in the mess hall were all that were keeping him vertical right now. Not that she needed to know that. He wanted Keller to focus on the woman in the isolation room and no one else today.

'You do know we'll update you the minute there's any significant change in Elizabeth's condition, don't you?' the doctor added, still trying to draw him into some form of verbal communication.

'I'll take another rest later,' he assured her. 'So, how's she doing?'

'Well, physically she's in great shape, and she seems surprisingly calm considering what she's been through...not that I know _exactly _what she's been through yet...but you know what I mean.'

'What about the nanites?' he asked, refusing to comment on that side of things just yet.

Keller called up the latest data she'd taken from Elizabeth just a few minutes ago, and brought the scan images up on a screen for him to see. 'The nanites appear to be functioning just as Dr McKay and I intended them to do. As you can see, the strongest concentration of them are in her brain, repairing the damage inflicted when the Asuran beam struck the city, and there are a few of them around in other places like her ribs and lung,' she circled an area on Elizabeth's torso with her index finger, 'which also suffered fairly extensive damage during the blast. But they're not showing any signs of acting beyond the initial instruction given to them. Of course, I don't know what else the little buggers are up to beyond what I can see, so if you want to check they're not sending out any kind of call to the other Replicators, Dr McKay's your man.'

Biting back his annoyance at her somewhat flippant tone, Sheppard nodded. If she and McKay hadn't been so reckless, they wouldn't be in this mess now. But he knew that wasn't the real him talking; it was the stress, the pressure, the nightmares, the sleep deprivation. The real him was glad to have his friend back no matter what her condition. He just wished he didn't feel so distrustful of her.

'I suppose I should go and speak with her,' he sighed. 'The other stuff can wait.'

'I think she'd appreciate that,' Keller said softly, reaching over the desk and giving his arm a gentle squeeze. 'I'll get you a hazmat suit.'

He shook his head. 'No. I don't want to go in there hidden under layers of crap. If I'm going in, I want to talk to her face to face.'

'But you know we haven't fully assessed the risk of the nanites –'

'They can't pass to me without physical contact, right?'

'I...I don't think so. I think it has to be a conscious decision to infect someone because the bond between some of the cells has to be broken to allow them to pass.'

'Well, I'll be sure not to touch her, okay?

Though she looked worried, Dr Keller seemed to know there was little point in arguing with him. 'Just be sure she understands the rules, too. If you come in contact with her at all, I'll have to put you in isolation until we can be sure you're not infected. You do understand that?'

'Of course. But you have nothing to worry about. Both Elizabeth and I are fully aware of what those nanites can do.'

'Okay. I'll make sure no one interrupts you or comes into the gallery until you let me know you've finished talking. It's going to be okay, Colonel. We'll get her through this. She'll be out of that room in no time.'

He tried to smile, but couldn't quite manage it, wishing instead that people wouldn't make promises they had no way of knowing they could keep.


	7. Chapter 7

Sheppard reached the door of the isolation room and hesitated in the sanctuary of that quiet corridor. What was he afraid of? It was Elizabeth sitting on the other side of that door – all the tests she'd undertaken so far had confirmed that. He was going to talk to a friend, that was all.

The two guards stationed either side of the doorway glanced at him, but said nothing. They obviously knew it wasn't their business to ask why he wasn't going in even though they were itching to do so; they were just there to make sure she didn't get out, nothing more. Taking a deep breath to steady himself, he waved his hand past the door control and it pulled back to grant him entrance.

Elizabeth lifted her head as the door drew back, looking worried as he approached and stopped a few feet short of the bed. She nodded and gave him a wry smile. 'At least you didn't come wrapped up in a hazmat suit.'

'Orange isn't really my colour,' he quipped, scratching his hair while he wondered what to do with his hands. He opted for plunging them into his pockets instead.

'It's good to see a friendly face without the distortion of a mask,' she said, her eyes fixing on him with such intensity that he found himself forced to look away. 'You always seem to know what to do to make people feel more comfortable. I've always admired that about you.'

He'd never been much good at handling compliments, not even from his friends. 'I think McKay would disagree with that assessment,' he snorted, feeling suddenly self-conscious.

'Ah, but even the way you play one-upmanship with Rodney is your way of bolstering him, isn't it? You know how much he enjoys that game.'

Clearly Elizabeth knew him much better than he'd realised. He smirked into his chest and nodded. 'I suppose he does.'

'And you spar with Ronon, even though you know he'll kick your butt.'

'Not every time,' he protested, but he knew it was true even as he denied it. Ronon always picked sports Sheppard was less skilled in and wiped the floor with him without fail, but he didn't mind. His friend enjoyed it, so he let him have his moments of victory.

'And then there's Teyla. You show her respect and listen to her advice– something that makes her feel a valued part of your team.'

'Well, she is...'

'And here, now, you've done the one thing no one else has dared to do since my return. You've shown you trust me. Everyone else comes in here suited up, but you just walk in here in your everyday uniform and treat this like it's just another conversation.'

'And that's what it is, isn't it?' he asked, peering at her from under lowered brows.

'You didn't tell Rodney to reactivate the nanites to save me, did you?' she asked, taking him by surprise. They hadn't really discussed the ins and outs of who had taken the decision to save her that way – there hadn't been time with the city dying around them – but he hadn't given the fact any thought since then. He supposed it was only natural she'd want answers.

'Why do you ask?'

'Because I know you, John Sheppard. You would never have done something so irresponsible while in control of the city. You would have said the risks outweighed the benefits, and you would have been right.'

He felt his face colour up at the strength of her belief in him. All through his military career he'd been criticised by his superiors for his rash behaviour, but Elizabeth had always believed in him, even after they'd disagreed on the best approach to problems, and there had been a few occasions like that in their early days on Atlantis. They'd had a bond, a shared understanding of the pressures of leadership, and through that bond they had grown to trust one another implicitly over the years.

'We didn't really have time to discuss it before leaving for Asuras, but I had some time to think about it after Oberoth dumped me on that planet. I realised you would never have sanctioned something so dangerous,' she explained.

'You were fading. Dr Keller had tried everything humanly possible to save you before coming up with the idea of reactivating the nanites. Rodney planned to program them to use raw materials from your own body to affect the repairs needed to keep you alive, but you crashed and he had to make a quick decision about what to do. He didn't want to lose you; none of us did.'

She nodded as she listened, catching his eye to make him look at her as she spoke. 'Where were you when all this happened?'

'I was helping Radek with some repairs to the station so we could reactivate the hyperdrive. There was a gaping hole to cross and we had to suit up to get across it, so there wasn't time to contact me and get the go-ahead.'

'Not that you would have given it.'

'Well, no, that's true.'

Silence descended on the room, and Sheppard wondered if, or rather hoped, it signalled the end of their conversation. He didn't do deep and meaningful, not even with people like Elizabeth, and was already feeling uncomfortable with the one-to-one situation they found themselves in. He longed for the casual ease with which they used to talk, the playful nudges, smirks, and jibes that had accompanied so many of their previous chats. Everything felt different now...

'You know you did the right thing leaving me behind with the Replicators, don't you?' she asked, reigniting their discourse.

He couldn't meet her gaze this time, worried she would see how much discomfort the thought of that event caused him. He felt he'd let her down, that he'd led her into danger and left her there to fend for herself, even though he knew there was nothing else he could have done. It wasn't a good feeling, and certainly not one he appreciated being reminded of.

'I'm not used to taking people out on missions and not bringing them back again,' he said quietly, kicking at something invisible on the floor. 'I wanted to come after you, but the IOA said it was too risky –'

'And they were right, just like you were right about the nanites. In an ideal world, none of this would have happened, and I would now be on my way home in a box. But it did, and if my having these damned things inside me means we managed to save the lives of every person on Atlantis, then I'm willing to put up with them.'

'The IOA wants me to question you about your time in Asuran hands. You think you're up to it?' he asked.

'I will be, just as soon as I've got myself cleaned up,' she replied with surprising cheer.

He smiled at that. Elizabeth was always immaculately presented, and the fact she hadn't had a chance to clean up properly in days was probably driving her nuts. 'I'll ask Teyla to get you some clean clothes and keep an eye on you while you freshen up,' he offered.

She forced on a wavering smile, then to his surprise, she burst into tears. He stood frozen to the spot, unable to approach her, although he wasn't sure what he would have done so even if he'd been able to.

'Oh...no...Elizabeth, please...please don't cry!'

'I'm sorry,' she sobbed, scrubbing the tears from her cheeks with the back of her hand. 'I promised myself I wouldn't do this...I don't even know why I'm crying. I should be happy for heaven's sakes. I'm just so relieved to see you again.'

Battling with his own fragile grip on his emotions, he nodded his understanding. 'You've been through a rough few days, Elizabeth. It's only natural you should need to let it all out.'

That brought another smirk to her face as she struggled to regain her composure. 'Not that you ever do that.'

He frowned, wondering where she was going with this line of conversation.

'You're the last person out of everyone I consider a close friend to come and see me, John. Rodney, Teyla, Ronon...they all stopped by yesterday to say how glad they were to have me back, even Radek put in a appearance, but there was no sign of you...not after you brought me here.'

'I'm sorry. I should have come, but overseeing the repairs to Atlantis is taking up a lot of my time.'

The look she gave him told him she didn't believe his story. It did sound pretty lame. Right now, they were completely devoid of any external threat; there was no reason he couldn't have spared ten minutes from his busy schedule...not that he'd had that full a day other than dealing with her reappearance. He'd reported the development to Stargate Command, and only an hour later had been asked to update the IOA about the situation. They had agreed to allow him some time to assess the situation and come up with a plan to neutralise any potential threat, giving them regular updates of any progress or developments. That was half the reason he'd insisted on the feed from the isolation room to his office; at least that way he could give them up to date and first hand observations whenever they requested them. He was glad Elizabeth didn't seem to know he'd spent most of the day in his office watching her, though. He figured he'd feel pretty creeped out if he knew someone was observing him that closely.

'That's no excuse. You're right; I should have come to see you,' he conceded, dropping his head in shame.

'It wasn't meant as a criticism, John. Teyla told me you haven't been yourself since the mission to the Replicator home world, neither you nor Rodney have. I just meant that your not coming here to speak to me tells me you're not venting your emotions. I imagine you feel bad about leaving me behind. Am I right?'

Sheppard chewed anxiously on his bottom lip, grimacing at the thought of putting the guilt rattling through his mind into words. He wasn't an expressive man – thanks to his father's influence – and he doubted that was going to change any time soon. When his mother had died, he hadn't seen his father shed a single tear, although there were times at night, when he lay in bed unable to sleep because he missed her so much, he thought he'd heard him sobbing. There was never any sign of sentiment in the man the next day, though, so John had always left his suspicions unspoken. As a result, both he and his brother, David, had grown up fast, and neither of them wore their heart on their sleeve...unless bickering could be classed as a valid exchange of emotions.

'I should never have agreed to take you on that heist,' he said, his voice croakier than normal as he spoke. 'You were fresh out of the infirmary and hadn't had time to get used to your new circumstances...it wasn't fair on you.'

He heard her sigh and looked up to see the sadness in her eyes as she gazed back at him, gripping the edge of her bed tightly as if it helped her remain composed. 'I wanted to do it, John. And if you hadn't taken me along, I doubt Atlantis would be in the fortunate situation it finds itself in now.'

'I know...that's what's so difficult for me to get my head round. I suppose somewhere inside I know leaving you was the only choice I could make, but...'

'...it wasn't easy.'

'No...no, it wasn't.'

She tilted her head to the side and smiled again. 'Well, maybe now you understand a little of how I felt every time you took yourself off on one of your damned suicide missions to save the city,' she joked. 'You think I wanted to agree?'

He huffed a laugh out into his chest. 'But I'm a military man. I'm paid to put my life on the line.'

He looked up at her in time to see her nod of agreement. 'Okay; I take your point. But perhaps now you understand now how I felt when I had to leave you in Kolya's hands, knowing he intended to torture and kill you.'

Time seemed to stand still. They'd never openly discussed their feelings over that matter. They'd just written up their reports – clear, logical and detached – as if it had been any other day on Atlantis. He'd always suspected the events had made a greater impact on his friend than she'd let on, and that perhaps the reason she didn't speak of them was because she was afraid of making him emotionally shutdown even further than his natural instincts told him to whenever Kolya's name was brought up in conversation. The pain of that feeding had been far beyond anything he'd ever endured in his life. Nothing in his SERE training at Fairchild Air Force Base had prepared him for the pain he was exposed to in that cold and desolate Genii warehouse. In training, he'd been stripped, hooded, humiliated, left cold, hungry and thirsty for days on end, and deprived of sleep until he felt like his eyes would fall out of their sockets, but it hadn't even come close to the mental and physical strain of that feeding. At Fairchild, he'd known those interrogating him didn't really want him dead, and he'd kept that thought at the back of his mind throughout it all, knowing the utter degradation would make him stronger. The only thing that had kept him sane through Kolya's torture was the thought that the dehumanising agony of having the life sucked out of him couldn't last for more than a day because, being fed upon at three hourly intervals, he knew he would be dead before the next sunrise. Now, after her own brush with death, it seemed Elizabeth thought this was an appropriate time to tackle the subject. He only wished he felt the same way.

'Elizabeth, I gave you my authority command not to fulfil any demands Kolya made,' he said flatly, his body already beginning to shut down the anger and fear trying to surface.

'And I gave you my authority command to leave me behind on Asuras. Did that make you feel any less guilty?'

After a pause, he shook his head. No, it hadn't, because he still thought there should have been another way around the situation. He supposed she'd probably felt much the same way about the torture she'd watched him endure.

'It took me weeks of talking to Dr Heightmeyer to convince myself I'd done the right thing in not handing over Ladon Radim to Kolya. I hardly knew the man, didn't know if we could really trust him, and yet I chose to protect him over saving your life because of the promise of a Genii Alliance. As it turns out, it was the right call, but the nightmares and the second thoughts after seeing what Kolya did to you troubled me for a long time.'

He chewed his lip again, averting his gaze. 'I didn't know that.'

'No, well it's not exactly something I go around advertising,' she confessed. 'I know you won't want to use Kate, but you have friends who will listen if you ever want to talk...including me.'

Embarrassed by her offer, he just stared at his boots. 'I'll bear that in mind.'

'For about ten seconds,' she quipped, giving him her trademark smirk as he looked up at her. 'You're a good man, John Sheppard. You have a lot of friends on Atlantis, all of whom are willing to help you keep this place running until the IOA decide what to do. Make sure you use them. Don't try to shoulder everything yourself.'

'I know, and I will,' he assured her, wondering if that was another of those promises made with no way of knowing if it would ever be kept.

Unexpectedly, Elizabeth's tears welled up again, and she dropped her face into her hands to cover them from him. 'Oh, don't look at me...I'm such a mess,' he heard her muffled voice cry into her palms.

'No you're not,' he insisted, taking a step toward her, then remembering he couldn't get too close. 'Everyone understands if you need to cry. You almost died out there – alone...'

She lifted her head proudly and sniffed back more tears. 'I did, and I don't know how I would've coped if that jumper hadn't come by. I'd have been stranded there like Robinson Crusoe.'

'Well, maybe you would have found yourself a nice Man Friday to settle down with and raise a few kids,' he suggested, giving her his crooked smile as he rocked back on his heels.

She laughed at his joked, giving him a lingering look that made his cheeks burn. 'I'm so glad I made it back to you,' she said softly, with no hint of a joke in her tone.

Embarrassed, John shuffled his feet some more, pushing his hands still deeper into his pockets. 'Me, too. You know I'd give you a welcome back hug if I could, right?'

'Liar,' she smirked. 'Getting a hug from you is harder than finding a ZPM.'

'Yeah, you might be right about that. Look, why don't I go arrange that shower and clean clothes for you, and then we'll have that official 'chat' the IOA are so keen for us to have.'

'Sounds good. The sooner it's done the better.'

'Can I get you anything else?'

'No, I'm fine. You get back to your duties. This place doesn't run itself, you know.'

'Believe me, I know,' he assured her.

'Oh, and John. I want you to know that if the IOA decides my having the nanites inside me is too big a security risk and they ask you to disable them, I'm okay with that. I don't want anyone else in this city to come to any harm because of me.'

The thought sent a chill through him, but he hid it from her. 'It won't come to that, Elizabeth. We'll figure something out.'

'I hope so. But I wanted you to know if that's the decision the IOA makes, I fully support it. I don't want this to become just one more thing for you to bottle up. Understood.'

Sheppard nodded, his emotions surging within him, battling to rise to the surface. He turned away before they broke loose and didn't turn back as he reached the door, relieved their one-to-one was over and he'd emerged reasonably unscathed. But there was one feeling still nagging at him, one that would not go away or be ignored.


	8. Chapter 8

The lab was a hive of activity when Sheppard reached it. A group of their top scientists were huddled in front of a screen and, as usual, Rodney was holding court, telling them what needed to be done. His captive audience looked both alarmed and annoyed as he ran through everything still requiring their attention, his acerbic tone grating on some already fragile nerves, no doubt. But whether he was annoying them or not, they listened intently, taking down notes in various ways as he continued on with his lecture and scathing observations of the tardiness of their progress.

Sheppard was by no means a genius when it came to the internal workings of Ancient technology, or any technology for that matter, but it sounded like they'd suffered more damage than he'd first thought during their escape from Lantea. It left him wondering if they could possibly ever get the city running the way it once had, even with 'the smartest guy in two galaxies' organising and overseeing the repairs.

He hung back so he didn't disturb their discussions, some of which were rather heated as they debated the quickest and most effective ways of getting the station up and running to a point where they could make another jump if required.

Sheppard had actually been on his way to suggest they work that out, and the fact Rodney had pre-empted him worried him deeply. First Teyla, now Rodney; was no one feeling unconditionally happy to have Elizabeth back on base? Did everyone view her presence there as a threat?

The geek debate seemed to go on for an age, with Sheppard checking his watch at regular intervals and considering whether his time might be better spent elsewhere. The trouble was, everything else seemed to be going smoothly at that point. Major Lorne was overseeing all military aspects of life in the city, there was nothing untoward showing up on their long range scanners, and with Teyla supervising Elizabeth as she got cleaned up, there really was nothing else he needed to do...except read through the mountain of mission reports now piling up on his desk from the various reconnaissance trips to find potential allies and ZPMs. He decided they would do for bedtime reading since they might help to cure his insomnia. The most exciting thing he knew that had happened to any of the off world teams was getting chased back to the gate by something resembling a cross between a bear and a lion. Other than that, he figured it would all be pretty uninspiring. They'd get lucky and meet up with some useful locals soon, they always did, but right now they seemed completely alone in this part of the galaxy...at least he hoped they were.

Eventually, Rodney wound up the conversation in his usual brash manner, sending his minions scurrying away to carry out their delegated tasks. Only then did he realise Sheppard was in the room with them.

'McKay,' Sheppard said, unable to suppress a smirk as he saw the look of surprise on the scientist's face.

'Sheppard,' Rodney replied warily. 'What brings you down here? Shouldn't you be up in the control room doing 'command' things?'

'All done...everything is running like clockwork, so I thought I'd come here and get an update from you.'

'Oh, right...okay. Well, as you probably just heard, there are still several primary functions performing at less than their full capacity, so those are our priority. We need to be able to power the control chair and the shields, and although we got them up and running well enough to get us here, I think the landing may have shaken a few things loose.'

'I know, I know...I don't kiss so well,' Sheppard quipped, staring at the computer screen.

He felt McKay tense beside him, obviously unsure how to respond to that. 'Yes...well...under the circumstances I think we're all willing to forgive you moving a little too fast,' he stammered.

Sheppard rolled his eyes in the scientist's direction, arching an eyebrow.

'All right, all right, so you're better at those kinds of jokes than I am, Captain Innuendo,' Rodney admitted, firing up the program he wanted Sheppard to take a look at. 'I can get the shields up to protect about two thirds of the city so far, but the outer regions are still exposed,' he explained, setting a three dimensional diagram into a slow rotation on the screen. The shield covered the central parts of the city and extended out to cover most of the narrow walkways through to the outer buildings, but those structures themselves remained untouched by its protection. 'So, as you can see, we are currently vulnerable to infiltration or attack in those outlying sections until I can fix or bypass the circuits currently not functioning.'

'And are the sensors working out in those areas?'

Rodney shook his head, looking grim. 'Not as of ten minutes ago. Circuits all over the city seem to be dying as quickly as we can replace them. When I said vulnerable, I meant vulnerable.'

Sheppard nodded, trying to keep the image of the Asuran city ship approaching them out of his head. If even a handful of those Replicators got into the city undetected, they could take Atlantis down from the inside.

'Okay, we haven't picked anything up approaching on the deep space scans so far, but I think it might be an idea to double the security teams in those outer reaches for the time being, just to keep a visual tab on what's going on out there. I'll notify Lorne.'

'Good thinking...but there's more,' Rodney interrupted, holding up a finger to stop him. 'The hyperdrive circuits are fried and we can't fire any drones if we come under attack because the weapons system is off-line. Until I get all that fixed, we're little more than sitting ducks.'

That wasn't good. A few days ago all those things had been working. Now, as Atlantis settled into its new position in the galaxy, it seemed circuits that had held out following the damage from the Asuran satellite weapon were now giving up the ghost. 'Stay positive, Rodney. You've kept us all alive this far; I have every faith you'll continue to do so.'

Rodney gaped at him as if he was waiting for the punch line. Sheppard just clapped a hand on his shoulder to show he meant it, quickly snatching it back.

'This new-found maturity of yours is going to take some getting used to,' McKay grunted, returning his attention to the computer.

'I know. I'm not that comfortable with it myself, but it comes with the job title,' Sheppard replied, deadpan.

After toggling through a few more screens, Rodney peered up at him. 'Was there something else?'

Not sure quite how to broach the subject, Sheppard pulled up a stool and sat down at McKay's workstation. 'I was just wondering how _you're_ doing?'

McKay stared back at him, slack-jawed and bemused. 'What? Why? Has somebody been talking about me?'

'No, nothing like that. It's just that now I'm in command here, the welfare of everyone in the city is my concern. So, I thought I should ask how you're coping.'

'Seriously? You know, this is kind of creepy...it's like you've had a personality transplant or something.'

'Come on, McKay. I'm trying to do the right thing here. Just play nice, okay?'

'Hmmm, all right. I'm good, thanks for asking. Are we done now?'

'Are you sleeping any better?'

Rodney looked terribly uncomfortable with his continued questioning, but kept up his side of the bargain. 'A little better, I suppose.'

'So you didn't sit up all night working again?'

'Not all night...no. But I do find work is the only think that keeps my mind off –' His face suddenly dropped, and Sheppard's heart leapt into his throat as he wondered what his friend was about to say. 'This new you doesn't give hugs, does it? Because, really, that would be just too weird.'

Grimacing at the mere thought of it, Sheppard slapped Rodney around the back of the head, giving him his non-verbal answer.

'Ahhh, now that's more like it,' Rodney quipped, apparently more comfortable now even if he did have to rub his head because it smarted from the contact. 'Now, if you'll excuse me, I've got a million and one jobs to do...' He turned back to his laptop and began to key in instructions.

'There is one other thing,' Sheppard ventured, watching Rodney's shoulders tense as he stood hunched over his computer. 'You went to see Elizabeth yesterday, right?'

Rodney turned back to him, nodding. 'Yeah...I wanted to tell her I was sorry about getting her in trouble with the Replicators...even though it wasn't strictly my fault.'

'How did she seem to you?'

Rodney narrowed his eyes, clearly trying to work out if Sheppard's words had some hidden meaning he was missing. 'She seemed good. Why, are you worried about her?'

'No...not exactly.'

'What do you mean, not exactly?' Rodney demanded, his anxiety mounting. 'Is she showing signs of going 'dark side' on us because that's not the kind of thing you should keep from people?'

Sheppard sighed, throwing his paranoid friend an angry frown. 'I'm the one asking how you think she is, Rodney. Did she seem normal to you?'

'Yes...I suppose. How about you?'

'Yeah...yeah. And how do you feel now we have her back?'

'Well, how do you feel?' McKay fired back at him.

'Rodney!' Sheppard growled, his green eyes flashing with anger. 'I'm trying to assess your feelings on this. If you keep asking how I feel first, you're just gonna say what you think I want to hear.'

'Oh, so now you're a psychologist, too?' McKay countered

'McKay!'

'All right, all right. I suppose...I suppose I don't feel as happy to have her back here as I thought I would.'

At last, some honesty, something he could get a handle on, and something he could understand because that was exactly how he felt, too. 'What is it that's stopping you from feeling happy?' he pressed, wondering if Rodney's concerns were the ones both he and Teyla shared.

'I don't know...' McKay whined. 'Perhaps, it's just that finding her seems to be...well...too convenient. Why did the Replicators let her go like that? Surely they could find more uses for her than dumping her on some uninhabited planet to rot or provide a meal for the indigenous wildlife.'

'Yeah...I'm having trouble with that myself,' Sheppard confessed.

They both stared at each other, Sheppard wondering what was going on inside McKay's overworked mind. He looked frightened, angry, worried, all in one great whirl, and Sheppard supposed he was feeling all those things, too, though he didn't want to admit it. He wanted to be pleased Elizabeth was alive and well, but this scenario had 'trap' written all over it.

'Do you think there might be some way of reprogramming those nanites to do what you originally planned now, you know, using materials from inside Elizabeth's body to repair the damage done in the blast.'

McKay's eyes drifted away from his as he thought about that, and Sheppard could almost see him computing the calculations and problems involved in that kind of reprogramming. 'Well, I suppose if I'm not up against a tight deadline there's no reason I couldn't write a program to do that. It would involve doing the repairs gradually and then getting the nanites to recognise when they're finished and shut down, but it's not impossible. Of course, I'll have to consult with Dr Keller to make sure they carry out the repairs in a viable way, and with the minimum disruption to Elizabeth herself, but gimme a week or two and I can probably work something out.'

'That long?' Sheppard asked, hoping this was one of those occasions when Rodney was being conservative with his estimate of time so he could look good when he did it much faster.

Rodney, rolled his eyes, his expression changing instantly to his normal scowl. 'Oh, I'm sorry to disappoint you, but brain surgery on the nanoscopic level isn't quite as simple as you might imagine.'

Sheppard rolled his eyes and counted to ten, his tried and tested way for dealing with one of McKay's fits of choler. 'You don't say. Look, just try and fix them sooner rather than later, okay?'

'And is this more important that fixing the hyperdrive, the weapons systems, or the shield generators, because, honestly, I'm not sure I should make that call.'

'Delegate, Rodney. You have a good team of people capable of helping with those other things. Use them.' He heard echoes of Elizabeth's warning to him as he spoke, realising he still trusted her more than he imagined he did

'Delegate...yes...I suppose I can do that,' Rodney nodded, scratching at his head as he tried to figure out the best person for each job.

'But before you get going on any of those things, I need your help. The IOA are keen to get to the bottom of what happened to Elizabeth while she was in Asuran hands. I'd like you to sit in on the interview, too.'

'Me? Why?' he asked, looking surprised as well as mildly concerned.

'Because protocol states there should be two members of Atlantis' crew present, and I think hearing what she has to say first hand will help you to come to terms with the part you played in things,' Sheppard told him.

He watched as McKay's jaw drop a little way. 'Oh...right...well, when you put it that way...I'll go get my Hazmat suit.'

'No. No hazmat gear. I want Elizabeth to feel as comfortable as possible when we speak to her. If we're sitting there looking like we're scared she might infect us, that isn't going to help her to relax, is it?'

'No...no...of course. You want me to ask someone to set up the recording stuff?'

'I'd appreciate that, Rodney.'

Rodney winced at the show of gratitude. 'You know, I'll be glad when we get our new commander in place. Then you can get back to normal and stop being so nice. It's unsettling.'

'Amen to that,' Sheppard laughed, hopping off the stool and following McKay out of the lab.


	9. Chapter 9

Teyla paced outside the patient's shower in the infirmary, waiting for Elizabeth to finish. She contemplated the breakfast she had shared with her teammates, a strange and strained affair considering the fact they had Elizabeth back among them. John had been particularly quiet, his face pinched with worry and fatigue. Rodney, too, had been much less vocal than usual, though he had managed to moan about how he practically had to fix everything because the other members of his team were incompetents in comparison to him before finally clamming up completely. Ronon, though amused by Rodney's rantings, had said very little, but that was not unusual and had proved something of a comfort to her.

Now, she was standing in a cordoned off area, with armed guards either side of it to ensure no one got in, and Elizabeth didn't get out. Her hazmat suit felt stuffy and uncomfortable, but Dr Keller had insisted she wear it as she might be required to help Elizabeth in some physical capacity should she fall ill while taking her shower.

Fifteen minutes had passed and it was quiet inside the shower room, so Teyla decided to shout through the door and make sure everything was as it should be. 'Are you all right, Dr Weir?' she called out, her voice sounding odd to her within the confines of her rubber headwear.

'Yes; I'll only be a moment,' Elizabeth replied, sounding unnecessarily apologetic for the time she was taking. Teyla didn't mind waiting for her in the least. After several days without proper food, water, or anywhere to get clean, she could completely understand Elizabeth's desire not to rush the process.

She leaned back against the wall, pondering whether or not to take off her helmet for just a moment to release some of the heat building up inside it and scratch the itch in her hair she'd been trying to ignore for the past ten minutes. But she was under strict instructions not to put herself at any kind of risk of contamination, so she decided to continue to ignore the itch as best she could. Instead, she thought about her conversation with John the previous day, the one when he had admitted he'd wanted Elizabeth back more than anything in the world. That was the most intense emotion she could ever remember him expressing, and the memory brought with it a surprising surge of resentment.

For some time now, since John had been infected with the retro virus and had swept her up into an overwhelming and slightly aggressive kiss, she'd been harbouring desires for him to show a sign that the feelings that had surfaced were not merely caused by the infection. Sadly, he'd not looked at her with anything other than respect or friendship since that day, much to her disappointment. Even their Bantos training sessions had dwindled over the past year, and he rarely found time now to accompany her to the gym and practice his skills. She missed the camaraderie those sessions had incubated between them, their time alone, and the opportunities for closeness and physicality. It was rare they spent any time alone now; their conversation the previous evening had been the first time in weeks.

A smile crept onto her face as she recalled some of their earlier sparring sessions when he had been all enthusiasm and almost no talent. She'd taken great pleasure in swatting his backside with ease to show him the ineffectiveness of his defence. She'd sensed how much that annoyed him, but it was hard to resist, he was so attractive when brooding and humiliated.

Of course, she'd not confided her true feelings for John to anyone in the team, in fact, the only person she had discussed her secret longing with was now dead. She sighed as she remembered Dr Houston, a fun loving scientist she had become from friends with over the three years they'd worked together. The scientist had often urged her to be honest with John because he was obviously not going to make the first move, but Teyla knew him better than that. If she ever admitted how she felt, he would only withdraw even further from her. There were regulations governing such things, and though he was not averse to bending the rules, that was one she felt certain he would uphold.

It had come as quite a shock when Ronon had asked her if she'd known John had been married after the memorial service for Carson, but it was just one of the many missing pieces in the puzzle that was John Sheppard. The fact he hadn't shared the news he'd been married in the past with anyone but Ronon, and then only after almost two years of friendship, suggested it hadn't been a happy experience for him, and probably explained his reticence to become emotionally involved with anyone. The only person he'd shown any genuine affection for was Cheya, the Ancient who had deceived them all to win the opportunity to spend time with him, but she had proved unattainable, and the whole experience had left him even less willing to show his true feelings for anyone.

Another wave of what felt like jealousy swept over her as she recalled meeting him on his way to share a picnic meal with the woman. He'd clearly been embarrassed to be caught in the act of wooing her, but she'd forced on a smile and told him he was allowed to have feelings for people without having to justify them to others. As she'd returned to her room after bidding him an enjoyable night, tears had stung her eyes and she had been unable to sleep for hours. Back then, only weeks after meeting him for the first time, she had still held out hope that they would form a relationship closer than friendship, but as time had passed, she'd realised his focus lay elsewhere. John Sheppard was a man devoted to his job; he put protecting people above everything else, including his own happiness.

Working alongside him had been both pleasurable and tortuous for the past three years. Her early desires hadn't been entirely without foundation; there had been signs of interest from him. When she'd first spoken to him in her home camp she'd felt a definite spark between them, and when he'd found her necklace in the abandoned city and helped her to put it on, his fingers had lingered a little too long on her coat front and his eyes had held hers just a moment longer than had seemed appropriate for a stranger who sought only trade and friendship. She'd felt certain their alliance would blossom into something more, and it had seemed he wanted the same thing, but, after the Wraith attack on her village and the loss of Colonel Sumner, John had taken on responsibilities that changed his outlook on their mission. He'd taken Teyla into his team, and she'd agreed to work with him because the thought of not doing so had been too painful to even contemplate. But their working relationship had overshadowed anything she'd hoped to find with him, and though their friendship had been a comfort to her when her people had moved to the mainland and left her behind, it simply wasn't enough. Sucking in a shuddering breath, she realised now with startling clarity that she still wanted more from him.

'Teyla?'

Elizabeth's voice made her start, and she pushed up away from the wall where she had stopped to lean. 'Elizabeth! Is everything all right?'

'Yes, everything's fine. You seem to be a million miles away, though.'

'I was just remembering happier times,' she said, giving Elizabeth a smile. 'Things have been so trying lately it is hard to remember them.'

'Yes...I know how you feel.'

Teyla was suddenly wracked with guilt for sharing her feelings with Elizabeth, whose problems were clearly far worse than hers. 'I'm sorry, Dr Weir. You do not need the added burden of my concerns.'

'Don't apologise, Teyla. You can share as many of your worries with me as you like – it takes my mind off my own problems!'

When she looked into Elizabeth's intelligent green eyes, Teyla saw only compassion there. It made her feel terrible for resenting the attention John was giving to her, the sleepless nights he was experiencing since her troubles had begun, and the fact he had wanted her back 'more than anything in the world'. She wondered if anything would ever erase those words from her memory, or the pain they caused whenever she recalled them.

'Come, I should escort you back to the isolation room. I understand Colonel Sheppard is going to record an interview with you.'

'That's right,' Elizabeth replied, walking along with her as two armed personnel slotted in behind them. 'The IOA don't trust me, and I can't say I blame them.'

Teyla forced on a smile. 'I'm certain that is not true. They are an organisation that thrives on information. I'm sure they simply want to document your experiences in the hope of better understanding what has happened to you and helping you.'

Elizabeth let out a little laugh. 'Oh, Teyla. I can always count on you to try to find the silver lining in every dark cloud. But I see how everyone looks at me. None of you trust me...not completely.'

'That is not true –'

'Come on, Teyla. Can you honestly put your hand on your heart and tell me you haven't had doubts about what happened to me?'

Teyla hesitated, instantly regretting the fact she had to reach for words when speaking to someone she had long considered a friend. 'We all have questions, but now you are feeling well enough, I'm sure you will be able to give us the answers we seek.'

The corridor seemed to stretch out far longer than usual as they made their journey back to the isolation room. Teyla had always loved the city of Atlantis from the very first moment she had set foot on it, but now it didn't feel as safe as it once had. The Asurans had almost destroyed them, and Elizabeth carried within her the building blocks of their society. It was impossible for them to feel completely at ease while those Replicator units were still active within her. Even the sunlight streaming in through the tall windows did little to cheer her mood as she contemplated just how dangerous the life form keeping her friend alive was.

'Teyla, can you do something for me?' Elizabeth asked, interrupting her thoughts.

'Of course – what is it?'

'Look after John for me. I get the feeling this is very difficult for him and he's under a tremendous amount of pressure.'

Forcing down her jealousy, Teyla smiled her agreement. 'I will. I know both he and Dr McKay are struggling with the increased responsibilities our fight with the Replicators has placed upon them.'

'Well, those two usually end up bearing the brunt when problems arise here. John never wanted to be in charge of Atlantis itself, and he needs to allow other people to share the responsibilities, not try to do everything himself. Talk to him...let him know you are all there to help. I've told him so myself, but he respects you, Teyla. If you tell him the same thing, I'm sure he'll listen.'

Teyla felt heat burn in her cheeks at the suggestion Elizabeth thought she and John were that close. 'I think you underestimate the esteem he holds you in. If he won't do something after you have recommended it, I doubt I could sway him to do otherwise.'

'Well, apparently I'm not the only one who's underestimating the esteem I'm held in,' Elizabeth smirked. 'Just promise me you'll speak to him; that's all I'm asking.'

'I will,' Teyla agreed.

When they arrived at the isolation room, Teyla found Sheppard and McKay were already in there waiting for them to return. Sheppard turned as they entered, watching Elizabeth as she made attempts to preen her wet locks into place. Teyla recognised the body language. Elizabeth cared about what John thought of how she looked. It seemed she cared about him much more than she'd ever let on in their personal conversations, but she could hardly fault her for that; she'd kept her own feelings for the colonel secret from Elizabeth, too.

As Teyla watched his reactions to Elizabeth, his expression passing through worry to compassion, his eyes then drifted to her. 'Is all that really necessary?' he asked, gesturing toward her suit.

'Dr Keller insisted I wear it in case I was required to physically assist Dr Weir. Had she slipped or fallen ill, I would not have been able to help as quickly as I could when wearing this.'

'Right,' he said, but she could see he wasn't entirely happy with the reasoning.

'Dr Keller was absolutely right, John. We can't afford to be careless until you're certain I pose no threat,' Elizabeth added, giving Teyla her whole-hearted support.

'Erm...maybe I should just go and...' Rodney stuttered, thumbing toward the door.

'Rodney,' Sheppard growled, throwing him a killer look. 'As long as we don't make contact with her, there's nothing to worry about. You don't need a suit.'

'Yes...yes of course,' Rodney nodded, but Teyla could see he was unnerved by Sheppard's insistence they not wear protection.

The fact John had decided to reject the protection didn't surprise her, not now, not after the things she'd heard him say, but forcing Rodney to show the same level of support when he was often worried about catching something as minor as a cold seemed unfair to her. She made a mental note to discuss it with John at a more appropriate time. But right now, they had the IOA breathing down their necks for answers, and the colonel clearly wanted to get the task over with. She had no doubt that listening to what Elizabeth had been through would be trying for both men, but she hoped it might help them find some closure for the guilt they were both struggling to rid themselves of.

'I will leave you to carry out your interview,' she said, giving John her most reassuring smile. Then she turned her attention to Elizabeth. 'I will see you again later, Dr Weir. I hope this interview isn't too difficult for you.'

'I'm sure Colonel Sheppard will be gentle with me,' she joked. 'Thanks for your company this morning, Teyla.'

'You are most welcome.'

With a final glance to John, Teyla ducked out of the room and stood in the corridor as the door slid shut behind her. Slipping off her headgear, she took a few deep breaths of cooler air to steady herself. That final look the colonel had shared with her had conveyed the conflict he was battling with. This mistrust of Elizabeth he was trying so hard to deny was eating into him, and she could do nothing to assuage his doubts because she felt them almost as keenly as he did. In fact, some deeply disturbing part of her didn't want to alleviate his worries. After all, Elizabeth was coming between them.

Biting back tears of frustration, Teyla shook that thought away. Elizabeth was not coming between them. If their relationship was meant to be, nothing would have stopped it. The truth was, her feelings for the colonel were unrequited – hard as it was to bear, that was what stopped them being together.

Angered that she could stoop so low as to wish Elizabeth ill, she strode away to return to her room. An hour of meditation would return her inner balance and calm her frayed nerves. Then, she could banish these ridiculous thoughts and get on with the important task of supporting all her friends through this difficult time, regardless of her personal feelings for them.


	10. Chapter 10

John held back near the door, waiting for the drinks he'd requested to arrive. He knew how much Elizabeth liked her coffee, and it seemed only right to provide her with a cup since she was likely to be doing a lot of talking.

Rodney sat on a chair several feet away from her, making awkward small talk. Of course, he'd been told not to share anything about the condition of Atlantis with his former commander, not until she had jumped through all the hoops and proved she hadn't been compromised, but finding other things to talk about was difficult for him. McKay lived and breathed his work, and had no real hobbies as such. He did have Katie Brown, however, so focussed his conversation around her and the dinner they'd shared the previous evening. Although Katie wasn't his type, Sheppard felt a certain amount of envy that Rodney had someone to share his down time with, even if it had only been twenty minutes while grabbing a bite to eat. Sometimes, he wished he had someone he could turn to at the end of a long, hard day. Then again, considering how badly his marriage had turned out...

Elizabeth seemed genuinely pleased to have someone other than medics to listen to, someone who wasn't purely there to monitor her current health status. Sheppard experienced a moment of guilt because he was shortly going to have to bring things back on track and grill her about exactly what Oberoth had done in the short time she'd been in his clutches. This was so hard; if it had been anyone other than one of his closest friends he'd have had little trouble with it, but Elizabeth was the one who had shown faith in him when others had doubted his abilities, the one who had inspired him to even consider making the trip to the Pegasus Galaxy, although his ultimate decision had actually hinged on the flip of a coin. O'Neill had tried to apply pressure, had even set him away from McMurdo for a few days to get his head sorted about where he wanted his career in the air force to go. Yet, without her request to Colonel O'Neill that he allow him to go to Atlantis, he wouldn't have even had the opportunity to wonder whether or not he should go. He owed her a debt of gratitude for this opportunity, for this chance at a better life that the restricted roles the air force back on Earth had offered him. He'd grown so much since his arrival there. At first, it had all been a great adventure, but the bonds he'd formed with his team and Elizabeth had made it into something far bigger than that. Atlantis was his home, and the people there were his family. He felt the urge to protect each and every one of them...though for some that feeling ran much deeper he now realised.

A knock on the door announced the arrival of their refreshments, three cups of coffee and a selection of pastries. He hadn't asked for the food, but it did make him realised how hungry he was again.

'Oh, thank God!' Rodney gasped, jumping up and rushing over to choose from the plate. 'I'm so hungry my stomach thinks my throat has been cut!'

Sheppard snatched the tray back from his grasping hand, casting him a warning look. 'Perhaps we should let Elizabeth choose first,' he suggested.

Rodney backed off. 'Yes...we could do that,' he agreed, but Sheppard could see his eyes were still fixed on the largest pastry on the plate.

John set the tray down and let Elizabeth pick out a croissant to eat with her coffee. 'Thank you, gentlemen,' she smirked, flashing an amused look Rodney's way.

Sheppard collected the tray again, knowing Rodney wouldn't want to get too close to Elizabeth, and the scientist snatched up the apple and cinnamon Danish, the biggest thing available. He was devouring it even before he resumed his seat.

Rolling his eyes, Sheppard took what was left, setting it down on a small equipment table the technicians had wheeled into the room to set their recording gear up on. 'Rodney, you want to check the camera's focused so we can record this session?' he asked.

With his cheeks bulging like a demented hamster, McKay nodded, licking his fingers clean of apple sauce as he lined up the camera to get a clear shot.

'Make sure you get my best side,' Elizabeth joked, primping her hair again and flashing Sheppard a self-conscious smile.

'Relax. You'll do fine,' Sheppard assured her, returning the smile.

He waited for her to finish eating, and then suggested they make a start; she nodded that she was ready and he set things running. Sheppard ran through the necessary information of who was present and stated the time and date index, then asked his first question.

'For the record, can you state what happened four days ago during the mission to retrieve a ZPM from Asuras, in your own words.'

Elizabeth swallowed deeply, then cleared her throat as she began. 'Four of us, that is Colonel Sheppard, Dr McKay, Ronon Dex and I embarked on a mission to acquire a functioning ZPM from the Asurans. After sustaining damage in the Asurans' attack, Atlantis was adrift in space and unable to continue its journey to the designated site without the power a ZPM could supply. Dr McKay had reactivated the dormant nanites in my body to save my life due to the grave injuries I suffered during the Asuran assault, and realised we might be able to use them to gain a tactical advantage. He determined that I might be able to tap into their systems and find a safe way in and out of their city, and I agreed to do it.'

Sheppard glanced to his right and saw McKay looking a little green around the gills, far from comfortable with reliving those moments. Hopefully he'd find a way to come to terms with his part in things as he listened to more of Elizabeth's story.

After taking a pause to sip her coffee, Elizabeth pressed on. 'The mission was going according to plan. We approached the Asuran city in a cloaked jumper and managed to land undetected. I was then able to steer Colonel Sheppard and Ronon through the city to the closest ZPM without them meeting any resistance. The mission went well and they returned to the jumper with the power source they needed. While they were en-route I was able to locate the original attack command the Ancients had programmed into the Replicators when they'd first created them. It was dormant, switch off by the Wraith themselves, but when I told Dr McKay what I'd found, he was able to writing a program to reactivate it. When Colonel Sheppard and Ronon returned to the jumper, we advised them of the situation, and the fact that reawakening the attack command might stop the Asurans trying to assault us again, so Colonel Sheppard said he would enter the instruction into their systems. He moved the jumper to the area of the city where we could access the Replicator base code, then Dr McKay extended the shield downwards into the city to shield our activities while Colonel Sheppard and Ronon transferred the unlocking sequence into the Asurans' system. Unfortunately, things didn't go according to plan and several complications arose, meaning the colonel and Ronon would be trapped and unable to return to the jumper with the power source we so desperately needed. I knew it was in my power to do something to help, so I headed out to intercept Oberoth and stop the Asurans from finding them.'

John felt his throat constrict painfully at the memory of seeing her holding the huge Asuran and his minions at bay, so fragile and yet so determined. Beside him, Rodney fidgeted in his seat; apparently the memories of his role in all this were still giving him trouble, too. This interview wasn't having the beneficial effect on either of them he'd hoped for.

'Can you clarify what happened after that?' Sheppard asked, urging her to finish the story up to the point he already knew. The IOA already had three reports explaining things from their point of view, but he felt it was important for Elizabeth to make her take on things known, too.

She nodded, pushing her drying locks behind her ear as she looked down at her feet. 'On their way back to the jumper, Colonel Sheppard and Ronon located me and tried to rescue me and get me to safety. But I realised if I released my hold on Oberoth to retreat it would put the whole mission in jeopardy. I made the decision to stay and ordered Colonel Sheppard and Ronon to get back to the jumper with the ZPM.'

She paused, pressing her lips together as she stifled her emotions. It was evident the recollection of being left behind was painful to her, too, and he wondered what it was about that situation that caused her the most difficulty.

'Colonel Sheppard...'

She stopped again, and John felt Rodney's eyes burning into the side of his face. He turned to see the accusatory look on his face, as if the upset Elizabeth was experiencing was all down to him, Sheppard resisted the urge to point out he wasn't the one who had activated the nanites and put her in that situation, and Elizabeth continued.

'Colonel Sheppard was reluctant to follow my instruction, but thankfully realised it was more important to escape with the ZPM than it was to extract me, a decision I was in full agreement with.'

Sheppard knew what she was doing. His action to shoot Colonel Sumner, even though he knew in his heart he had seen the colonel give his consent, had caused him years of grief and regret. She knew superior officers, critical that he had made no attempt to save the man, had pulled him up on the act. But there had been nothing left to save; he'd witnessed that, but those _superior officers, _and he used the word 'superior' in the loosest possible sense, who had never had the misfortune to meet the Wraith found that impossible to accept. This time, she was making sure whoever saw this recording knew Sheppard had acted with her full consent, and his choice to leave her behind had not been any kind of attempt to work his way up the ladder of success. Not that he care about what anyone else thought of what he'd done; only her opinion mattered.

'What happened after the rest of your team retreated?' he asked, his stomach now churning in anticipation of her answer. His mind had been conjuring up all kinds of horrors since that fateful mission; now he was about to find out if what he'd imagined was anywhere close to the mark.

'Oberoth was furious, of course. He wanted to go out after you, but with the jumper cloaked he had no way of tracking where you had gone. So he did the next best thing. He probed my mind for clues about where we'd been headed before we'd come to our unscheduled stop.'

'Should we be worried?' Rodney asked, his voice quavering slightly, though he did his best to mask it.

She shook her head fervently. 'No. I would have told you immediately if they'd forced any information from me.'

'Can you be certain they didn't?' John asked. He didn't like to make her think he didn't trust her, but the Asurans had ways of convincing you of things that weren't true, so they couldn't take any chances.

'I don't suppose I can't be one hundred percent sure that they didn't get something from me, but I know I didn't give anything away voluntarily...no matter how persuasive they tried to be.'

'What do you mean?' Rodney asked, his face blanching.

She seemed to shudder as she cast her mind back to recount what had happened to them, and John steeled himself to hear about the abuse she'd endured.

'First off, they just probed my mind, making the process as uncomfortable as they could, over and over. I think they thought they could grind me down just with the sheer pain and confusion it caused. It was like someone shoving barbeque skewers into my head as far as they would go. But the nanites active in my brain kept me strong. Each time they thought they were getting somewhere, I just threw them a false memory, or something banal that was no use to them at all. I don't think they were too impressed with the memories I shared of hosing Sedge down after he took a particularly sticky mud bath.'

Sheppard smiled at the thought of just how unimpressed Oberoth would have been, but at the same time couldn't help but be afraid of how powerful Elizabeth had become in her own right if she could block the replicators' attempts to gain information over a protracted period of time. He knew only too well the physical strain that put on a body.

'When they realised hurting me wasn't going to work, they moved on to hurting people I cared about, feeding me images of my mother, Simon, you people – all of you suffering horrendous torture at their hands, or having accidents, or falling prey to the Wraith. But they couldn't convince me any of it was real. I'm not saying it didn't hurt to see those things anyway, but I could see through the images to what lay beneath and I held on to the fact it wasn't real and it got me through. I knew I had to get back to you...to all of you.'

It was a minor correction, but it stopped Sheppard in his tracks. She'd been looking at him as she spoke, and the fact she felt compelled to adjust her wording seemed to suggest she thought she'd said too much, as did the colour now burning in her cheeks as she averted her gaze to the floor. Thinking he was reading too much into it, Sheppard glanced over at Rodney, seeing the same surprise in his reaction. Momentarily stunned, Sheppard couldn't think of any more questions he needed to ask.

Looking decidedly uncomfortable, McKay cleared his throat and broke the silence. 'So, what kind of things did they make you see?' he asked, his sense of the macabre kicking in as it always did. Though he had a morbid fear of pain and death, as any sane man would, he also had an odd fascination with it, as if he might find clues to some great unsolved mystery if he learned enough about it.

Snapped out of his shock, Sheppard was quick to step in. 'You don't have to answer that, Elizabeth. I don't think we need to know that level of detail.'

'Well, if the IOA want me to recount it some time, I will. But I'd prefer not to have to recall those things unless I have to,' she admitted. 'The important thing is they didn't fool me.'

Keen to wrap things up, Sheppard brought the questioning back on line. 'When they didn't get anywhere with that tactic, what did they do?' he asked, struggling to keep his body language as open as it had been prior to her 'slip'.

'That was when they decided to abandon me on that uninhabited planet. They knocked me out and transported me there while I was unconscious. When I woke up I was sitting in the dust all alone and their jumper was soaring away from me. At first I thought it was another illusion they'd created to trick me, but when I tried to see through it, to detect the programming behind it, there wasn't any to see. That was when I knew they'd left me there to die.'

'That's inhumane...even by their standards,' Rodney gasped.

But Sheppard was more concerned with another detail. 'So you were unconscious for a while?'

'Yes.' Her large eyes lifted now and held his confidently. She had no fear that he meant to catch her out. She appeared to trust him implicitly, answering as honestly as she could.

'So it would be fair to say there was a substantial length of time when you were unaware of what the Asurans were doing to you.'

'Yes, it would be fair to say that,' she agreed, 'But I doubt they can access information or memories from an unconscious mind since they can have no way of manipulating it.'

Any other unconscious mind, perhaps, but since her neural pathways were held together by nanites, he suspected it might not be that black and white. Sheppard shared another glance with McKay. The look of horror on the scientist's face told him Rodney had come to the same conclusion.

'Interview terminated at 10:35 hours,' Sheppard announced, bringing the session to an abrupt end. 'Thanks for that, Elizabeth.'

She looked surprised it was all suddenly over. 'Is that it?' she asked

'Yeah. I think that's as much as we need for now,' he replied, flicking her a tight smile as he helped McKay to gather up the equipment. 'I'll send Keller along to check you out in a moment.'

She nodded, but he could see she was shaken by his sudden desire to be out of the room. He wondered if she, too, now recognised the significance of what she'd said. He hoped not; he was scared enough for the both of them right now. He didn't want her to worry, too. Or perhaps she sensed the other reason he needed to put space between them...

'Will you come by and see me again soon?' she asked. 'It would be nice to chat on a less formal basis.'

Though he wasn't sure if he could handle that, he made himself agree to her request, knowing he wouldn't want to let her down once he'd given her a promise to be there. 'I'll stop by before I turn in for the night.'

'Thank you,' she said, but her face was sad as she gazed at him, silently expressing the same wish he had – the wish that things could be normal between them again.

He swallowed down the lump of anxiety building in his throat and grabbed the mobile table full of recording equipment, sweeping from the room with Rodney close on his heels.

'Is there any chance they could have tampered with Elizabeth's nanites while she was out?' he asked the scientist as soon as the door had closed.

'Well, there's always a chance, but I haven't found any sign of it,' Rodney told him.

'Is it possible they built in some kind of time delay, you know, to lull us into a false sense of security and then take us down when we drop our guard?'

'Yes...yes, I suppose they could have, but so far I can find no sign what-so-ever that they tampered with her at all. Is it so hard for you to believe that they really did think she was insignificant enough to abandon out there? You know arrogant they are. They look at us like we're some kind of nuisance to be swatted out of existence. They're probably off chasing the Wraith right now as we speak.'

'Yes!' Sheppard snapped. 'It is too hard to believe. They knew she was Atlantis' leader and what the kinds of information she potentially held. I honestly can't believe they would toss her out like a piece of garbage after only one day of trying to break her.'

'But that's probably because the attack code kicked in. And you saw her in there, Sheppard. There was no sign of subterfuge in anything she said. Well, other than that one thing...'

Sheppard knew he was referring to her correction, and refused to be drawn into conversation about it. 'The Asurans aren't the only ones guilty of arrogance, McKay. You still refuse to accept that their technology is way beyond our full understanding.'

'Be that as it may, I'm sure she isn't lying. That's still our Elizabeth in there.'

'No, she isn't, Rodney. Don't you get it? While those nanites are inside her, she can never be 'our' Elizabeth. She can't lead Atlantis, can't be involved in any decisions on the future of this place, she can't even be briefed on what's going on with the city at the moment. And while she can't play any part in this city's life, she is not 'our' Elizabeth. Now, I want you to get back to that lab of yours and find a way of fixing her and shutting those nanites down. And I don't want it to take two weeks. Is that clear?'

'Well, it's clear, but it's also impossible. These things take as long as they take, Sheppard. I can't just wave a magic wand and wish the damn things away!'

'Find a way to do it, Rodney,' Sheppard ordered, pushing the table of recording equipment into Rodney's midriff by way of an order that the scientist should get the material they'd gathered to where it needed to go.

'Now you're really starting to sound like a commander,' Rodney hissed

'I'll take that as a compliment.'

As he strode away, Sheppard heard McKay call out after him. 'You blame me for all this, don't you?'

He faltered to a stop, every nerve in his body buzzing with the desire to punch something – anything – to relieve his frustration. He took a deep, calming breath, and without turning called back, 'We all played a part in this, Rodney. Now we all need to do whatever it takes to fix it.'

'So, are you going to just ignore what she said to you in there?'

Closing his eyes, Sheppard tried to imagine why Rodney would think now of all times was a good one to push him on that. 'I'm not having this conversation with you Rodney,' he warned. 'Now get your ass back to the lab and get working...and make sure your people make the hyperdrive their priority. I think we may need that sooner than we thought.'

Silence followed. He hoped he'd said enough to make Rodney push himself just that little bit harder than he already was. They were relying on McKay to sort this problem out; Sheppard had no doubt about that. He was good at dealing with things he could point a gun at, but these things were so tiny and insidious he knew nothing he could do would make a difference. Once again, the pressure was on McKay and his science team to get them out of a horrible mess. He just hoped they all had enough strength left in their reserves to see them through.


	11. Chapter 11

_Sheppard lay in his bed and stared up at the dark ceiling, imaginary shadows swelling and retracting as his tired eyes tried to pull details into focus._

_He'd visited Elizabeth just before 22:00 hours, just as he'd promised, finding her still looking as fresh as she had that morning when he'd interviewed her. Those nanites kept her going when any average human would flag, and he found the fact they did so hugely disconcerting. They'd spoken for around ten minutes about nothing of any consequence – the weather, surfing, dogs and other such trivialities – always skirting the subject touched on that morning, but he'd sensed she was already growing tired of being cooped up in the same room all day. He could hardly blame her, but until the IOA gave the go ahead for them to remove the isolation protocols, they had no choice but to keep her there. Not that he minded the delay; he felt they needed more time to make a full risk assessment before releasing her into the city._

_He closed his eyes, pressing the heels of his hands into them and muttering, 'Switch off, John. Get some sleep!'_

_Of course, the more conscious of the fact he still wasn't asleep he became, the less likely it was he would relax enough to go to sleep. He huffed out a sigh and threw himself onto his side, screwing his eyes shut and refusing to check the time again. The time was irrelevant; only the fact he was still awake mattered._

_A gentle, electronic chime announced someone at his door. He lifted his head and stared at it for a moment or two without moving, wondering who could be bothering him at this later hour. If it was something urgent, he would have had a message via his earpiece rather than someone coming to visit him. The chime repeated and, realising whoever was out there wasn't about to go away, he cast his sheets aside and trudged over to the door to unlock it._

_When it drew back to reveal Elizabeth smiling at him, his breath caught in his throat and he couldn't speak._

'_Hey, you. Did I wake you?' she asked, peering past him at his dishevelled bedclothes._

'_Er...no...no...not really,' he said, raking his fingers back through his hair. 'I haven't got to sleep yet.'_

'_Well, I just wanted you to let you know in person that the IOA have decided I haven't been compromised in any way during my time with the Asurans, so I'm free to retake my position as Leader of the Atlantis Expedition.'_

_His jaw dropped at the news, and he mentally groped about for an appropriate response that wouldn't cause her offence. 'Really? That's great. But I'm surprised they didn't tell me themselves considering they asked me to fill your boots for a while.'_

'_Oh, don't be like that, John. I thought you'd be pleased for me,' she pouted in a manner far too flippant for the situation as far as he was concerned. 'Besides, you didn't really expect any courtesy from them, did you?'_

_He supposed he didn't, judging by their past record, but that didn't make it right. 'I am pleased for you, Elizabeth. I just think they should've spoken to me about it. Who did they report back to?'_

'_Does that matter?' she asked, blinking her long lashes at him innocently as she held his gaze._

'_It matters to me, yes,' he replied, pushing past her. 'I think I might just contact the SGC and find out why I was bypassed.'_

_He felt her hand land on his shoulder before he could get more than a couple of paces. 'There's no need for that, John. Everything is just as it should be now. Accept it and things will be much easier for you.'_

'_What are you talking abou –?' He gasped as her fingers dug into his shoulder, pressure forcing him down to his knees. With one hand, she'd rendered him immobile; he could literally feel his bones crushing under her grip._

'_I have control here now, and soon my Asuran brothers will join us and destroy this last great symbol of Lantean civilisation. I wanted you to be here to see it, but if I can't trust you to hold your peace...'_

'_I won't...let you...destroy...this place,' he grunted, panting against the pain. 'I will...stop...you.'_

_He reached for his sidearm, but she kicked it away before he could even level it at her. Not that it would have slowed her for long; he'd only intended to use it to distract her while he got free and called for reinforcements. She released his shoulder, but only long enough to circle him and swing a right that knocked him straight on his backside. The bitter tang of blood hit his tongue and stars dotted his vision. It felt like she'd hit him with a baseball bat. _

_Spitting out the taste of it, he pushed back from her with his feet, too stunned by the blow to stand. She tracked him, smirking as she finally planted her booted foot on his chest and pushed him flat to the floor. 'I'm sorry, John, I really am, but I can't have you running around Atlantis telling people what we're up to. Still, maybe I don't have to kill you. Maybe, if I have a little feel around in that head of yours I can help you to forget.'_

'_No!' he yelled, trying to force her foot off him, but she was too strong. She bent forward, crushing the air out of him, extending her hand toward his forehead and pushing it in excruciatingly slowly as he screamed for her to stop..._

Sheppard fell out of bed, still flailing at an arm that didn't really exist. Hitting the floor woke him with a start, but it still took him several more seconds to realise he was safe in his room and not in Elizabeth's clutches. He gasped in much needed air, and once his heartbeat slowed to a pace that didn't suggest he might arrest, he untangled himself from his bedclothes and half-staggered, half-crawled, into his bathroom.

Absently rubbing at his sore backside, he ran a sink of water to freshen up before realising he didn't even know what time it was. He checked his watch. 0502 hours. That was the longest he'd slept in days, though he didn't feel any better than he had when he'd gone to bed. Soaping up his chin, he shaved, then jumped into the shower to wash away the sticky feeling coating his skin. That done, he dressed and heading out to start the day.

He thought about going straight to the mess hall to grab an early breakfast, but then reconsidered. His dream had left him a little unnerved and there were other more important issues on his mind than food. He had a few things he wanted to check out, so he turned around and headed for the labs, hoping to find someone he could put his questions to. It wasn't exactly a surprise when he got there and found Rodney already hard at work.

'Morning, Rodney,' he called as he approached, forcing on a smile.

'You're up early,' Rodney muttered, as he finished what he was doing.

'Not as early as you, apparently.'

Rodney looked up now to face him. 'God, Sheppard. You look terrible.'

'Thanks for that,' Sheppard grunted, leaning on Rodney's workstation and planting his free hand on his hip as he glared at him.

'Yeah, well...I say what I see, you should know that by now,' the scientist said by way of an apology. 'Anyway, what are you doing here?'

'Thought I'd come for an update.'

'At 05:20 am?'

'I'm awake, you're awake. What's the problem?' Sheppard asked.

'Nothing,' Rodney replied with a sigh, calling up the file containing the latest reports from their repair teams. 'Okay, well, we've been concentrating on repairing the power relays first. We think we may well have them fully functioning before the end of today which means we should be able to extend the shield to cover the entire city.'

'That's good news.'

'Yes, it is. Unfortunately, since the hyperdrive is still off-line, should the Replicators locate us and send another of their satellites, it won't be able to protect us for long. They could soon drain the ZPM and leave us vulnerable again.'

'I'm really starting to hate that word,' Sheppard grumbled, rubbing his jaw.

'Yeah, you and me both.'

'So how about the hyperdrive?'

Rodney called up another file and quickly studied the contents. 'Well, apparently the hyperdrive sustained extensive damage during the flight and landing, and we have to improvise a few new circuits to replace some that are completely shot. That's going to take a few more days, hence the need for the shield.'

'Okay...well...we'll just have to hope the Replicators don't turn up until we can get the city mobile.'

'Yeah. Like I said before, our luck has to change soon, right?'

'Right,' Sheppard agreed. 'So, just supposing we're wrong and the Replicators came and infiltrated the city. Could we overload a naquadah generator to disable them the way we did with the Ancient nanovirus?'

Rodney winced, no doubt recalling the several hours he'd spent thinking he was going to die, then shook his head. 'I know a pulse shut down Elizabeth's nanites after Niam infected her, but those nanites were isolated units, and hadn't replicated enough and formed strong enough bonds to take complete control. The sheer numbers involved in human form replicators means they have an immunity to the effect of an EM pulse. What we would need to do is create a new disruption frequency to break the bond between each individual nanite, and we'd need a way to ensure they were all caught in the disruption field at the same time so they couldn't adapt and resist it.'

'And you can do that, right?' Sheppard said hopefully.

Rodney zoned out for a few seconds, giving the matter some thought. 'Yes. If I could find the right frequency, then we could do something similar to what we did in the jumper on Asuras. I could program it into the ARG crystal, and then change it for the one that generates the city's shields. As long as we can extend the field to cover the entire city, I should be able to get it to sweep through as far out as the full extent of the shield.'

'Sounds good.'

'Well, it would be...if I had enough time to do it. I'm still working on reprogramming Elizabeth's nanites so they can be shut down and leave her alive. Are you changing my priorities again?'

Sheppard chewed pensively on his bottom lip. 'I may be, yeah.'

'Oh, well let me know when you decide,' McKay hissed.

'I'm changing them,' Sheppard announced. 'I want you to work on the disrupter _and_Elizabeth's nanites.'

'Oh, okay. And when did we add another twelve hours to the day?' McKay spat, folding his arms over his chest and glaring at him.

Sheppard wasn't at all fazed by his tantrum. 'It's all about time management and delegation, Rodney. Oh, and just out of interest, if we couldn't get the disrupter up and running, and if people on Atlantis were to be infected by nanites the way Elizabeth was, we could shut them down with a naquadah blast, right?'

'Yes. As long as one of us could get to a jumper and get it up to the right height, and as long as we caught the spread early enough,' Rodney agreed, calming with the distraction of the question.

'Okay. Thanks, Rodney. If you could look into that disrupter problem, I'd be grateful.'

He began to walk away, but Rodney called after him. 'You don't think the Asurans are finished with us yet, do you?'

Sheppard turned to face him again, wondering how much to say. He wanted to tell his friend about the dreams he was experiencing that constantly pointed to the dangers of having Elizabeth on board Atlantis, but he seriously doubted Rodney would sympathise. He kept his answer simple.

'I don't know any more about the Asurans' plans for us than you do, Rodney. All I do know is I can't think of a single reason they would have let Elizabeth go so soon that doesn't lead me to the conclusion that this is some kind of ambush waiting to happen.'

'Well, I've been doing a lot of work on those nanites since you asked me to reprogram them, and there is absolutely no sign they are in any way different from when she went on the heist to Asuras.'

Sheppard couldn't help but smirk at the scientist's assuredness. 'But you didn't have full control of them then, McKay. If I recall, you couldn't activate the 'kill' switch when we needed you to and you had no idea why,' he pointed out.

Faced with that evidence, Rodney had to concede. 'No...no...that's true. But they certainly aren't communicating on any subspace frequencies, so they're not giving our position away.'

'Maybe they don't need to,' Sheppard muttered, pondering just how much damage the nanites in Elizabeth alone could do if they began to spread.

'The nanites are showing no signs of acting under their own intelligence, Sheppard. You're worrying about nothing,' McKay tried to assure him. 'I wrote their code myself. They are no threat to us as they stand.'

Sheppard forced himself not to roll his eyes at the sound of Rodney's arrogant assertions. Much as he knew Rodney was right that the nanites were safe as long as they kept doing just what they were doing now, he also knew his subconscious was telling him there was a risk here, a danger that he shouldn't ignore. Still, until he saw signs of a real problem, there was no point in alarming Rodney with his fears, so he just nodded his agreement. 'I know, Rodney. Like you said, we just have to hope the other Replicators don't find us, and then we're home and dry.'

'Exactly,' Rodney said, giving him a lop-sided smile. 'I'll put some time into that disrupter, though –just in case.'

'That would be good, Rodney.'

'Er, are you going to get some breakfast now, 'cos if you are I can join you.'

Sheppard checked his watch, but decided 05:30 hours was just too early to start eating yet. 'No. I thought I would go check out things up at the control room, maybe run through any security issues with Major Lorne, then I'll get an update on Elizabeth's condition. Why don't I meet you there in an hour?'

'Okay. It's a date!' Rodney grinned, then cringed as Sheppard shot him a shrivelling look. 'Of course, by that I didn't mean a 'date' date...oh, you know what I meant!'

'See you later, Rodney,' Sheppard said, heading out the door before he laughed. Rodney really was bad at the whole friendly banter thing; even worse than he was, and he hadn't thought that was possible. That was probably why they gelled so well – two socially challenged individuals supporting each other through the minefield of friendship.

On his way to the control room, he stopped and stepped out onto one of Atlantis' many balconies to enjoy a few moments of the early morning air. The sky was blue, but broken up by cirrus clouds reflecting the warm tones of the sunrise. It was a beautiful view, but he couldn't fully enjoy it until he'd ascertained there was no Asuran ship lurking among the wisps of colour. His subconscious was warning him something was coming; his sixth sense for trouble had kept him safe so far in situations where others had perished, so he couldn't ignore it now. He just hoped Elizabeth wasn't central to whatever trouble was looming as his dreams were suggesting she was. She had to survive this.

After coming so close to losing her he realised how desolate Atlantis seemed without her there. The city was ailing, and it felt like fixing it depended on fixing her. Her dream had brought this place to life, and he hoped the nightmares he was now troubled by weren't a sign that it was all about to come to a terrible end. Whether the bond he and Elizabeth shared was more than friendship, he still wasn't sure, but he felt a strong connection to her, something he didn't want to lose again if it was in his power to stop it.

For now, he would have to take his mind off things by carrying out his duties, and later he would watch the feedback from the cameras in the isolation room again. Painful as it was to see her cooped up that way, it was more painful to speak with her face to face right now. Everything that had happened over the past week had unlocked feelings in him he hadn't realised he'd been suppressing, but now they had definitely surfaced, and were raw like an exposed wound. What was worse was the fact Elizabeth seemed to feel the same confusion, and now he was aware of that, distancing himself seemed all the harsher. But it had to be done. He was the current commander of Atlantis; he couldn't put himself in unnecessary risk or allow himself to become distracted by personal issues when so much was riding on him to get them all through this.

'Colonel Sheppard. Ms Shen of the IOA wishes to speak with you. I've been asked to patch it through to your office so she can talk to you in private,' a young female voice said through his earpiece. He recognised it as one of the women who worked in the control room, but whose name he'd neglected to learn. He made it a priority to do that today. He needed to be more personable with them all now he was in charge.

'Copy that. I'm on my way,' he replied, pushing back from the rail.

Taking a last, deep breath of the morning air, he ducked back inside to get the chat with the IOA out of the way. He'd been dreading this moment, and hoped they would allow him the extra time needed to find a solution to the nanite problem before insisting they be shut down. Now, it was time to find out just how accommodating they were willing to be

*****

When he got behind his desk and activate the channel to the SGC, he found Xiao Shen gazing back at him, looking as pristine and composed as she always did.

She gave him a tight smile, though her eyes remained cold. 'Good morning, Colonel Sheppard. I hope I didn't disturb you calling so early in the morning.'

'Not at all. I was already awake,' he assured her, giving her an equally unfriendly smile.

'I see. I suppose there is a lot to do there at the moment. How are the repairs coming along?'

'As quickly as can be expected,' he replied before deciding to cut to the chase. 'Have you reviewed the interview with Elizabeth?'

Shen straightened up in her seat, apparently surprised by his directness. 'We have,' she told him. 'In fact, we spent many hours discussing the matter. You do realise how serious a threat Dr Weir now poses to the security of Atlantis?'

Sheppard bit back the urge to ask her just how big an idiot she thought he was, and kept his response to a diplomatic, 'Yes, we all realise that. As you know, she's being kept in isolation, and anyone making physical contact with her is expected to follow full hazmat protocols. The nanites can't spread even if they wanted to, which, apparently, they don't.'

'So you feel the situation is contained for now?'

He ignored the unease that churned in his gut at the sound of that question. 'In my opinion, yes.'

'So as yet you see no reason to deactivate the nanites with immediate effect?' Shen asked, her eyes showing no sign of compassion as she said those words, as if she were talking about killing off a computer virus and not a human being.

John recognised the look as that of a person who could happily hide behind rules to commit the most heinous of acts if it were deemed necessary. Well, she might be prepared to let Elizabeth go, but he wasn't about to give up on her just yet. 'No. Both Drs McKay and Keller are monitoring the nanites on a regular basis, and there has been no change in their function. We will, of course, review the situation should that change. At the moment I have Dr McKay working on a way of healing Elizabeth using her own cells so we can shut the nanites down without killing her. I think she deserves that chance, don't you?'

Shen didn't answer that. 'And if deactivation of the nanites became the only viable option, would you be able to authorise that?'

Her eyes burned into him, and Sheppard realised what she was referring to. 'If the lives of the rest of the crew of Atlantis depended on it, I would have no hesitation,' he assured her.

'Are you certain of that, Colonel? It has come to our attention that your relationship with Dr Weir might be more...complicated than either of you has declared.'

Sheppard sucked in his cheeks and struggled to hold back the rant forming in his mind. The IOA had never been completely happy with the arrangement in Atlantis, and he certainly wasn't the first choice for military command. Now they probably thought they had a reason to finally remove Elizabeth from the picture, and perhaps him, too. Once again he kept his answer as civil as his growing anger would allow. 'I'm not sure what you're basing this assumption on, but I can assure you the relationship between myself and Dr Weir has never been anything but professional. If you're looking for a reason to remove me from my post, you're going to have to come up with something better than that.'

Clearly unimpressed with his tone, Shen brought their discussion to an abrupt halt. 'I believe I have said all that needs to be conveyed to you at this time, Colonel Sheppard. Continue the good work. Oh, and I would very much appreciate it if you could arrange for Dr McKay to brief us on his progress in the next scheduled update.'

Before he could respond the laptop screen went blank, leaving Sheppard with the almost irresistible urge to stamp it into oblivion. How dare that woman tarnish Elizabeth's character when she was already suffering so much? He didn't mind the bashing his own ego had taken because he was in a position to defend himself, but Elizabeth wasn't, and Shen didn't seem to care.

He sorely hoped McKay could pull off the miracle they needed and fix her, that way the IOA wouldn't get the opportunity to replace her after all. That would really give Ms Shen something to be so po-faced about.


	12. Chapter 12

Ronon blocked the assault, bending to the side as a second Bantos swung toward the space his head had occupied only a split second before. He swung for his opponents legs, but missed when they leapt into the air, his sparring partner landing lightly before making another attempt to crack him around the head.

After blocking further shot from his opponent's Bantos sticks, he sidestepped and brought his stick in behind his combatant, cracking Teyla across the backside. She sucked in a breath through her clenched teeth, rubbing her injured rear.

'You're off your game today. What's up?' Ronon asked as she limped to the window seat and picked up a towel to dry her face and arms.

'I confess I am rather distracted this morning,' Teyla admitted sadly, facing the tall glass window of the gym as the light coming through it bathed her in its warmth.

Teyla was one of the most focused people Ronon knew, especially when it came to sparring. It took a lot to put her off, so she obviously had something serious on her mind. 'You still worrying about Elizabeth?' he asked.

'It is a continuing concern, do you not think?' she asked.

He shrugged. 'Sheppard has it in hand.'

Teyla didn't respond to that. She just turned her back to him and wiped her face. In fact, it looked to him like she was drying her eyes.

Wondering how best to play this situation, he decided he couldn't ignore it. 'You sure you're okay?' he asked, circling her so he could see her face again.

Sure enough, her eyes were red-rimmed and she sniffed back more tears as she lifted her face to his. 'It is nothing for you to be concerned about, Ronon. I am simply tired and overwrought following our recent brush with the Asurans.'

He realised then that the source of her woes might not be Elizabeth herself, but the man he had just mentioned prior to her tears.

'Sheppard'll get us all through this. I have every faith in him,' he reiterated, and once again she seemed to respond to the use of his name, her eyes immediately filling with tears. 'Teyla – did something happen between you and Sheppard?'

She looked suddenly alarmed, clutching the towel to her chest. 'What do you mean?'

'Well, twice now I've mentioned his name, and twice you've started crying. I'm thinking that's more than just a coincidence.'

She turned away again, staring at the window rather than looking at him. Evidently, whatever was playing on her mind was difficult for her to talk about.

'Did you two have a fight? Because, you know he's under a lot of strain right now and whatever he said –'

'We did not fight,' Teyla said quietly, still facing away from him. By the way she began sniffing again, he know the tears had started to flow once more.

'So what is it?' he asked, stepping forward and placing his huge hands on her slight shoulders to demonstrate his support. He felt her suck in a shuddering breath, then she reached up and took one of his hands in her delicate fingers.

'You are a good friend, Ronon. But I fear this is something I can share with no one.'

'If I'm such a good friend, you should be able to tell me anything,' he pointed out. Then, he turned her to face him, wiping a tear from her cheek with the back of his fingers. 'Whatever you say to me goes no further than this room, I promise.'

She averted her gaze and pressed her lips together as he watched her ponder whether she really dared to tell him what was troubling her so much.

'Before you joined us,' she began, stopping to take a breath and steady herself, 'back when the Humans first arrived on Atlantis, John was not in command of the military personnel of Earth. He was under the command of Colonel Sumner. Has he ever mentioned him to you?'

Ronon shrugged. 'He mentioned his name once, but I got the impression he didn't want to go into any details about him.'

'Colonel Sumner led a military team through the Stargate to my home planet of Athosia to meet with us and discuss trade. Though I was introduced as the leader of our people, Colonel Sumner looked through me as if I were not there. But John,' she smiled reverently as she recalled the events, 'John spoke to me so warmly that I instantly felt he was a man I could trust and allow to become a friend. Soon after their arrival, Colonel Sumner and I, and several others of my people and the Human troops, were taken during a Wraith attack on my village. John put his life on the line, flying a jumper onto the Hive ship holding us in an attempt to rescue us all, but he could not save Colonel Sumner. The Wraith had fed upon him, and he was close to death. John helped ease his passage from this life, they helped the rest of us to get off the ship. It was later, when he told us what he'd done, that I realised he was someone I could truly pledge my allegiance to. Only the strongest of men can kill someone out of mercy, knowing they will carry that memory with them for the rest of their life. After that, Atlantis gave refuge to my people for a while, but when they chose to move on, I knew I had to stay...not just because I felt I could make a difference here, but because...I could not bring myself to be parted from him.'

Ronon felt his eyebrows twitch up a degree, but he kept his reaction even. 'You never told me you felt that way before.'

'No, I did not wish it to affect the dynamic of our team.'

'Why didn't you ever tell him?'

Teyla sighed, and rolled her eyes to the ceiling. 'Because after a short while it became evident John did not feel the same way about me. All he wanted from me was my friendship and my assistance; I had misread the signs.'

'I don't know. I always kinda thought you two would get together. I even told Sheppard as much –'

'Really,' she asked. 'What did he say?'

Ronon gave her a grim smile, sorry to snatch away the small glimmer of hope his words had awakened in her. 'Nothing much. It was the day Carson died. The first explosion happened just as he was about to tell me.'

Her shoulders slumped. 'No matter. I already know the truth. He sees me as a colleague and friend, nothing more. His feelings lie elsewhere.'

Ronon wondered what she meant, but then realised there was only one thing she could mean. 'Dr Weir?'

Teyla nodded, her eyes brimming with tears again. 'His reaction to her loss was clear enough, but now she has returned...it seems he can think of little but her. Nothing else is important to him now.'

Her words surprised him. 'You're jealous?' he asked, finding it hard to imagine Teyla reacting that way to anything; she was always so calm and rational...the exact opposite of him, in fact.

'I...I do not know. I am usually so controlled in my emotions, but when it comes to John...yes, I suppose I am. I even found myself wishing Elizabeth ill yesterday because I begrudged the attention he was giving her. I never imagined I could think anything so shameful.'

'Why don't you just tell him how you feel – get it out in the open?' Ronon asked.

Teyla rolled her eyes to the ceiling again, stifling a sob. 'Because I know he would withdraw further from me. At least this way, keeping these feelings to myself, I am allowed to work alongside him and protect him where I can. But I cannot help him or protect him from the pain he is feeling now. She is all he thinks about. I believe he is...in love with her.'

'But they're both leaders here. Neither of them would allow anything to happen that could interfere with their jobs,' Ronon pointed out. 'Sheppard has always been specific about that with all the military under his command. No relationships that compromise work.'

'That does not change the fact he wants to be with her...and if that is how he feels about Elizabeth, then...'

'I get it,' Ronon said, cutting her off before her voice cracked and the tears brimmed over again. He thought about what Teyla had said. Sheppard had, indeed, been distracted since Elizabeth's return, and there might be some truth in her belief that their relationship ran deeper than he'd ever let on. The colonel and Elizabeth had always been close, but it could simply be that Sheppard was wrapped up in the potential danger Elizabeth's presence on Atlantis posed and that was why he was giving her so much of his time. And it appeared now that it wasn't just a physical danger; Elizabeth's presence was pulling Sheppard and Teyla apart. He wished he could say something to help, but he suspected there was nothing he could do to ease his Athosian friend's anguish. This was one problem she had to work through herself.

'Why don't we go get some breakfast?' he suggested, picking up his own towel and mopping the sweat from his face.

'Yes, I think perhaps I am feeling hungry now. Maybe we could collect John on the way?'

Ronon nodded. 'No problem. I just wasn't sure if you'd want to.'

'I cannot avoid him in a place like this, so I feel my best option is to continue as we always have. I would hate to give him any additional cause for concern at this time. He carries a great enough burden as things are.'

'That's probably best,' the Sateden rumbled. 'I'll get a shower and meet you outside.'

*****

Later, as they walked toward John's room, they spotted Rodney in the corridor ahead of them, speaking quietly with Dr Heightmeyer.

Teyla caught Ronon's arm and gestured that they should hang back, allowing their friend the time he needed to speak to her in private.

After a couple more minutes of discussion, he turned their way and noticed them, winding up his conversation quickly then heading in their direction.

'Morning. You guys heading to the mess hall?'

'Yes. We are just on the way to collect John,' Teyla answered.

'Well, you won't find him in his room,' Rodney told her, rocking from his heels to his toes. 'I saw him up and about almost an hour ago...' He stopped, eyeing them both suspiciously, noting their attire and wet hair. 'Have you two been to the gym already?'

'Yeah, what about it?' Ronon asked, fixing him with one of his stares.

'It's not even six-thirty in the morning. You two are some kind of masochists,' he grumbled, checking his watch.

'Do you have any idea where John was going?' Teyla asked patiently.

'Three guesses,' Rodney snorted. 'Where has he spent most of the past two days?'

Ronon felt his hackles rise at Rodney's flippant tone. Sheppard was obviously uncomfortable with taking on the full leadership role, and he didn't see how Rodney's sarcasm was helping things.

'His office,' Teyla sighed, her shoulders dropping.

'That'd be my best guess,' Rodney nodded. 'Although I suppose I should feel honoured that he visited me in the lab first.'

'What did he want?' Ronon asked, intrigued as to why Sheppard would have sought out Rodney so early in the morning.

'He asked for an update...which I gave him. Then he started asking about ways of stopping the Replicators if they got onto Atlantis. He wants me to work on a Replicator disruption weapon so we have a defence against them if they should infiltrate...and he wanted to know what we could do if the nanites spread through the crew...huh, and people call me paranoid!'

'There has been no sign of the Asurans since we arrived here, and nothing to suggest Elizabeth's nanites are able to replicate beyond their current numbers. Why is he so concerned with these things? Surely, if the Asurans knew where we are they would have attacked us by now?' Teyla asked, voicing Ronon's own thoughts.

'I don't know, but I think having Elizabeth here in her current condition is making him edgy...there's something really strange going on between those two at the moment. Did he tell you that during the interview we did the other day she actually said the thought of getting back to him kept her strong?'

Teyla rolled her eyes and sucked in a sharp breath, wrapping her arms around herself as if they somehow provided defence against the agony of those words.

Feeling annoyed that Rodney had thrown that into conversation so casually, Ronon frowned down on the scientist. 'So?' he demanded.

'Well, did you guys know there was something going on between those two, because I didn't? I always thought Elizabeth had a thing for smart men!'

'You mean...like you?' Ronon smirked, folding his arms over his chest.

'Well, not _just_ me,' Rodney started, then he shut up as Ronon's continued staring made him anxious.

'Colonel Sheppard is considered an intelligent man by many people,' Teyla pointed out, leaping to Sheppard's defence.

Ronon was grateful Rodney was apparently too thick skinned to notice how agitated Teyla was with his attitude. It might have given away more of her own feelings for Sheppard than she wanted to share if he weren't.

'Yes, but he's not exactly in my league,' Rodney snapped defensively.

'Maybe you're too smart for her,' Ronon suggested. 'She might be intimidated by your mind.' He said it as a joke, but quickly realised Rodney was seriously considering his suggestion.

'Hmmm, yes, that's possible. And I suppose Sheppard does have a certain roguish charm,' the scientist mused. 'Women seem to like that kind of thing, don't they?'

His eyes darted to Teyla, and her mouth fell open a little. Ronon immediately stepped in to change the direction of the conversation. 'Well, why don't stop all this speculation and go to the mess hall and to see if Sheppard's made it there now?' he rumbled, pushing past Rodney and heading on down the corridor.

'Well, I _am_ pretty hungry,' Rodney agreed, hurrying along behind him.

Ronon checked over his shoulder to make sure Teyla was also in tow. She was coming along, but hung back, probably in an attempt to avoid further awkward questions about Sheppard's appeal with the ladies. Rodney's timing, as was often the case, was as bad as it could be.

At the door to the mess hall, they bumped into Dr Keller. 'Oh, hey! Are you all going in for breakfast?'

'Yep. I'm here to gird my loins ready for the day,' Rodney said, patting his stomach and giving her a crooked grin.

'Mind if I join you?'

'No...no...the more the merrier,' he said, without consulting either of his companions.

Ronon looked over at Teyla, watching her eyes scouring the room, but he'd already worked out Sheppard wasn't there. He supposed the colonel could pull up an extra chair and join their table when he did show, so put a hand on Teyla's shoulder and guided her in. 'Come on, Teyla. He'll get hungry sooner or later.'

She nodded, giving him a sad smile as she allowed him to steer her to the food counter. He noticed Rodney and Heightmeyer exchange a look as the scientist passed her where she sat alone at a table to the left of the room. He'd never known McKay to be the type to open up about his feelings, at least not since he'd had that weird thing happen with Cadman, but he was too troubled by the dilemma Teyla was facing to try to work him out. Things were going to come to a head soon, he could feel it, and he just hoped it wouldn't spell the end of their team when it did.


	13. Chapter 13

Sheppard snapped awake with his feet still resting on the desk in his office. Apparently, he'd been more tired than he'd realised on settling down to monitor Elizabeth, or perhaps the serenity of watching her sleep had sent him off into slumbers. Unlike him, Elizabeth still slept soundly, her chest rising and falling with each gentle, sleepy breath. She looked so peaceful, all the cares and worries of the last few days missing from her face as they always were when she slept. He wished she could experience the same peace of mind while awake, but after that interview and his chat with the IOA this morning, he suspected her troubles, perhaps all their troubles, were far from over.

He checked his watch, finding he was already late for his scheduled breakfast with Rodney. Bouncing up from his seat, he set off at a jog for the mess hall, keen to keep his tardiness to a minimum to avoid uncomfortable questions.

As he pushed through the door, narrowly avoiding a flustered Dr Biro as she made her exit, he spotted Rodney, Ronon and Teyla already eating along with Dr Keller. He supposed he couldn't be annoyed that he'd lost his seat since he was late, so collected up some breakfast and made his way over to them, planning to hijack a chair from the neighbouring table and join them.

'Good morning, Colonel Sheppard,' he heard a soft voice call to him. He winced, knowing exactly who those dulcet tones belonged to.

Stopping, he turned to greet Dr Heightmeyer. 'Morning, Doctor. Are you well?' he asked pleasantly, hoping that was enough to get him past her.

Unfortunately, it wasn't. 'I'm well, but I do hate taking breakfast alone. Would you mind joining me?' she asked.

Sheppard tried not to make it too obvious he was scanning the rest of the room and mentally calculating just how many free chairs there were at partially occupied tables. Twenty-six, he quickly noted. So why did she need him to join her?

'Er, okay...' he drawled, with the sense he'd been strategically ambushed. 'But I have to eat and run.'

He set his try down and slid into the chair opposite her, picking up his knife and fork and hoping to dive into his meal before she could start talking.

'How're you feeling this morning, Colonel? I hope you don't mind my saying so, but you're looking a little tired.'

Refusing to put down the food he'd just scooped up, Sheppard pushed it into his mouth and chewed it up before responding. 'Well,' he mumbled, pushing what remained of his mouthful into his cheek, 'I've had a lot to deal with these past few days. There hasn't been much time to fit in a full night's sleep.'

'Yes, I can imagine. So it's not that you can't sleep?' she asked, her eyes wide and innocent as she probed deeper.

He looked at the woman he'd spent most of the past three years deftly avoiding, and wondered why she was suddenly so interested. Peering over to his team, he saw Teyla casting him an anxious look, snapping her eyes away when she realised he was looking at her. Teyla saw Kate Heightmeyer regularly, and had often told him how therapeutic she found unloading her troubles on the softly spoken psychologist.

'Well, I do have trouble sometimes...but I'm pretty sure that's down to the pressure of having so much to do.'

He waded into his meal, pushing in a few more mouthfuls while Heightmeyer nibbled on the corner of some toast as she watched him. He could feel her eyes on him, but acted as if he was oblivious.

'I suppose having Elizabeth back among us must have caused you some pretty mixed feelings,' she pushed.

He lifted his eyes from his plate, meeting her sky blue gaze. Someone had been priming her for this conversation. Again, he glanced over at his team's table, and again Teyla quickly looked away.

He shrugged. 'I'll admit I wasn't expecting to find her so easily, but I'm glad she's back.'

'I suppose the IOA are nervous about things...especially because of the potential risk of the Replicator cells spreading.'

'Well, Elizabeth's nanites are showing no signs of multiplying, so I'm sure, given time, they'll relax about things.'

'And you?'

He frowned. 'And me what?'

'Well, if you don't mind my saying so you do seem very tense. A lot of people are worried about you, Colonel. No one wants to see you buckle under the strain. You know my door is open to you any time.'

_Actually, I do mind you saying that, and 'buckle under the strain'?_ _Is that what people really think is happening to me?_ He ran his finger around his collar, then tried to turn the movement into a casual scratch of his neck. This didn't feel like therapy, it felt like a...a violation. Did people actually find this helpful? 'I'm sure you're pretty busy at the moment, what with us all nearly dying lost in space a few days ago. I expect that kind of thing might have traumatised one or two folks.'

'But not you?' she asked, batting her long lashes as she watched him.

How should he answer that? If he said no, it made him sound cold, unfeeling even. But if he said yes it was an admission of weakness. Atlantis was under his leadership; he couldn't afford to get traumatised in times of trouble.

'Well, I'm trained to deal with life and death situations. Sure I get scared, but I have coping mechanisms I can put in place to deal with that. Some of the people here, the civilians, they haven't had that kind of training. I figure they need you more than I do right now.'

She smiled and nodded, seemingly happy with his answer. He wondered if that meant he'd passed whatever test she'd set for him.

'You must find all the administration in your new role a chore. You're a man of action, after all,' Dr Heightmeyer said, changing the subject.

He smirked as he ate another mouthful of scrambled eggs, holding back his laughter so he didn't spray her with masticated food. 'I have a pile of reports in my office that bare testament to just how tedious I find that part of the job,' he confessed. 'I plan to make a start on them this evening unless some crisis or other stops me. Personally, I'm praying for a crisis.'

She gave a genuine laugh, and her face melted into a far less patronising smile. 'You'll excuse me if I say I hope you get a lot of reports read.'

'Yeah, I guess I can forgive you.'

As he continued to eat, he saw his team begin to leave. Ronon passed him first, clapping a heavy hand on his shoulder in greeting, then Rodney rushed past, barely looking his way as he chatted with Keller. Teyla brought up the rear of their group, and he felt her eyes on him, but didn't acknowledge her. He was too angry about this set-up she'd manufactured to wish her a good morning.

'So, how are you feeling about having Elizabeth back on a more personal level,' he heard Heightmeyer ask as he finished up the last mouthful of his meal and swigged back his coffee.

After swallowing it all down, he said, 'I'm happy, of course.'

'You and she are close friends, aren't you?'

He eyed her, squinting as he tried to work out just what she meant by that. He'd already had enough accusations from the IOA about the possible inappropriate nature of his relationship with Elizabeth, he wasn't about to listen to the same garbage from her. 'We're _good _friends, yes,' he said pointedly replacing the word _close _with one he felt was more appropriate.

'I'm sorry. I didn't mean to cause offence —'

'You didn't,' he replied brusquely, cutting her off.

Heightmeyer fell silent and ate a little more of her breakfast, but Sheppard could feel her analysing him still. As far as he was concerned, she could do it in her own time; he'd had more than enough of her crap.

'Well,' he said, making a big show of checking his watch, 'This place doesn't run itself. Thanks for the chat, but I should get going now.'

'That's all right, Colonel. I have to see my first client of the day in less than an hour and I need some time to reprise myself on all of this morning's cases first.'

They parted company, Sheppard still fuming that Teyla had thought him so incapable that she'd put him in such an uncomfortable position.

*****

After checking in at the control room again, Sheppard headed up to his office and fell into the chair behind the desk. Elizabeth's belongings were no longer dotted around the place, and it felt somehow soulless without them. He'd briefly considered moving his Johnny Cash poster in there for decoration, just so it felt a little less cold, but now Elizabeth was back, he didn't want to give her the impression he was moving in on what had always been, and to him would always be, her territory.

He eyed the pile of reports, slipping the first one from the top of the tower and laying it flat on the desktop in front of him. With a sigh, he flipped it open and began to read, yawning as the banality kicked in within seconds. This was going to be a long day if nothing more exciting cropped up soon. He checked the time and promised himself a coffee break and a snack if he did two hours of reading first, as if that was all the incentive he needed to wade in and decimate the heap.

Minutes later his attention was wandering, and his eyes drifted to the office door, which he had left open as Elizabeth always had. From there, he saw Teyla walking past and on toward the stairs.

Jumping up from his seat, he darted to the door and called after her. 'Teyla! You got a minute?'

She turned, looking mildly worried, then smiled and nodded. 'Of course.'

He stepped aside to let her pass him and enter the office, then closed the door behind them. The significance of that action wasn't lost on the Athosian, her face immediately falling. 'Is something wrong, John?'

He took a moment to gather his thoughts before slowly turning and rounding on her. 'I don't appreciate the stunt you pulled this morning, Teyla. Please make sure that doesn't happen again.'

Confusion scored her brow as she looked back at him. 'I...I do not know what you mean.'

'You set me up with Heightmeyer at breakfast. I _do not_ need a shrink, understood? I'm not about to _buckle under the pressure_,' he made little quotation mark gestured with his fingers as he said the final four words, then planted his hands on his hips and glared at her.

Shrinking away a little under the intensity of his gaze, Teyla defended herself against the accusation. 'I had nothing to do with your encounter with Kate this morning,' she gasped, hand on her heart as if she thought that might make her protest more believable.

'Oh, come on, Teyla. You're always the one banging on about how good she is, and how beneficial you find your little chats. Well, that's all well and good for you, but I don't feel the need to unburden myself to her, so I'd appreciate it if you didn't discuss me with her behind my back.'

She fish-mouthed at him for a few seconds, trying to find the words to fight back. He'd never felt this angry with her before, but he'd never felt this betrayed by her either. She was supposed to be his friend; friends didn't do that kind of thing to one another.

To his surprise, Teyla now came right back at him, her dark eyes bright with anger. 'It is a good thing I did not react so harshly when you first suggested Kate talk to me. I would have missed out on so much help, and the chance of an empowering friendship.' Her eyes narrowed in anger, now. 'But you have never considered yourself as weak as I, have you? I am only a woman –'

'I didn't recommend you speak with her for that reason...you were...are...a valuable member of my team. I didn't want to lose you to stress!'

'Nor I you. But I would have thought you understood me better than this by now, John. I know how much you despise baring your soul. I would never place you in such an uncomfortable situation. Never.'

The final word was said with such vehemence and emotion that her voice cracked with the strain of it. Only then did it occur to him that he might have jumped to the wrong conclusion after all. 'But you were watching us,' he sputtered. 'Why were you so interested if it wasn't you?'

'I was worried. You have never sought advice from Kate before and I was concerned that you had a serious problem if you had gone to her for help,' she explained, clearly still angry with him.

Her argument made sense, perfect Teyla logic he realised, and he dropped his gaze to the floor to break the confrontation. 'I...I'm sorry, Teyla,' he apologised. 'I shouldn't have made assumptions.'

'No you should not have,' she said forcefully, and from the quavering pitch of her voice he could tell she was now fighting back tears.

He lifted his eyes again, seeing the moisture in hers. 'I really am sorry, Teyla,' he said softly, feeling a hitch of emotion clenching in his throat as he saw the sadness in her expression.

'Have I ever been anything other than loyal to you?' she shouted. 'Have I ever given you any cause to question my actions where our friendship is concerned?'

'No...no, never...'

'So why turn this aggression on me now? Why me and not Ronon or Rodney? They are your friends and were also there this morning.'

'Yeah...but Ronon and Rodney? Come on, they're not exactly big exponents of the therapy angle.'

'So, of course, it had to be me? Could it not have simply been that Kate is concerned after everything you have been through recently and offered her support freely?'

'I suppose that does sound reasonable,' he mused, chewing his bottom lip.

'Or perhaps Dr Keller spoke to her on your behalf. You have been to her for treatment, haven't you?'

She was still shouting, and as Sheppard looked out through the glass walls of the office, he could see a number of people looking their way, or working while trying not to look like they were listening in.

'Let's calm this down, shall we?' he said quietly, holding his hands up in mock surrender. 'I made a stupid mistake, and I am very, very sorry.'

'I am tired of always being there for everyone...of being taken for granted...of never having anyone consider my feelings in matters before decisions are made,' she continued to rant, tears now breaking free and running down her cheeks. 'Did you even once consider how I would have felt when you went on your mission to Asuras to steal the ZPM? Did you think about how afraid I was that none of you would return? I was actually relieved when I heard Elizabeth had been taken because it meant three of my four best friends had come home to me. Do you have any idea how terrible it is to feel relief at the death of someone you care about?'

'I...I didn't think about that...there wasn't time to do much thinking. I had to leave Atlantis in the hands of someone I trusted, and I couldn't think of anyone more trustworthy than you!'

'And yet here you are today accusing me of humiliating you...of thinking you cannot cope. How have you lost that trust in such a short passage of time?'

That silenced him. He had no answer to that. Why had he turned his annoyance on her? She was right; he should have known she would never do something like that behind his back. Teyla had always been his most loyal teammate. Annoyed at himself for causing her so much distress, he did something he never did; he reached out and took hold of her shoulders, gripping them to steady her. 'I'm so sorry, Teyla. I don't know what else I can say. You're right. I'm an idiot. I guess all this stuff with Elizabeth has got to me more than I realised.'

Calming, Teyla lowered her head toward him, and John recognised she wished to share the Athosian act of friendship with him. He touched his head to hers, feeling her shuddering breaths as she trembled against his brow.

When she lifted her head again to look at him, all the anger had drained from her, leaving only sadness where it had once been. He swallowed hard, and chewed his lip again, waiting for her to speak.

'I think, perhaps, we are all feeling the strain of the past week far more than any of us imagine. I just want you to understand that...that I would never do anything to hurt you, John. But I am tired of being taken for granted. I have feelings, too. I am not made of stone.'

'I know, really...I do,' he insisted. 'And I would never do anything to intentionally hurt you either.'

'Perhaps you should consider whether a less...negative view of Kate's abilities would help you rationalise things more clearly in this difficult time.'

'Yeah...maybe.'

Suddenly overcome, Teyla pulled him into a hug, pressing her face into his chest and sobbing until he felt her tears soak through to his skin. He reached around her, awkwardly seeking places to put his hands that couldn't be misconstrued as inappropriate contact, especially since the IOA had already accused him of being involved with Elizabeth. Teyla's preference for items of traditional Athosian clothing rather than the standard issue T-shirts other crew members wore left her skin more exposed than he was entirely comfortable with, and he tried not to think about how smooth it felt beneath his hands. Her hair smelled of apple-scented shampoo and she wore a perfume as light as air itself, reflecting her subtle femininity. For a while, he'd found it hard to work with her because of the instant and obvious attraction he'd felt. But, realising the battle with the Wraith was her priority and always had to be because she took the care of her people so seriously, he'd buried those feelings deep and learned to view her as a friend. He valued her friendship and hated the thought he had done anything that might jeopardise it.

Ronon appeared at the door now, looking puzzled to find them embracing. Sheppard saw him from the corner of his eye and took the opportunity to break the clinch, which had gone on for far longer than he was comfortable with already. 'Hey, buddy. Come on in.'

Ronon flicked his attention from one to the other of them, clearing his throat, then asking, 'Everything all right?'

Teyla wiped away tears on the back of her hands, nodding silently as she brought her tidal wave of emotion under control.

'Yeah, we're good,' Sheppard assured him, folding his arms across his chest. 'We had a little disagreement, but it's all sorted now.'

'What about?'

'It's not important now,' Teyla said, pushing stray strands of hair back from her face. 'I must get to the gym. I have a training session lined up and I am already late for it.'

As she headed for the door, Sheppard called after her, 'Teyla...we're okay now, right?'

'Of course,' she nodded, but he saw her face crumple again before she could fully turn away.

Ronon turned to face him with his normal, deadpan expression. 'What was that all about?'

'Just a misunderstanding,' Sheppard said, heading to the desk and sitting down to read the file he'd laid there.

'So I heard...all the way down the corridor.'

'So you know what it's about, then?' Sheppard grumbled, picking the file up, then throwing it back down again without reading a single word. He couldn't concentrate – not now.

'Not really. I heard raised voices, but these walls are pretty good at muffling the actual words.'

Sheppard tried not to look as relieved as he felt to hear that. He attempted to read the file again, then realised Ronon apparently wasn't planning to leave him alone to work.

'Was there something else?' he asked.

Ronon walked up to the desk, picked up the next file in the pile and flicked through it, dropping it back on top of the others. 'Are you really gonna read those?'

'Yeah...that's the plan,' the colonel sighed, his shoulders slumping as he looked at them. 'That is...unless you have a better idea.'

'You wanna spar?' the Satedan asked, barely masking his vicious smile as he peered up from under his heavy brows.

'D'you promise it won't involve me hopping on one leg?' Sheppard asked, squinting suspiciously at his warrior friend.

'Absolutely.'

'You're on!' Sheppard leapt out from behind his desk and was at the door before Ronon could even take a couple of steps. A good scrap with his friend was just what he needed to clear his head and help him forget the upset with Teyla. He couldn't believe they'd got into a screaming match. It wasn't like him, and it wasn't like her either. Did he take her for granted? He supposed he did. He did have a tendency to assume Teyla would always be there for him, and would support his decisions without question. But she clearly wasn't made of stone, just as she had told him. He would have to be more careful with how he treated her in the future. He didn't want to lose her support at a time when he needed it more than ever.


	14. Chapter 14

In the gym, Sheppard ducked as Ronon's staff whistled through the air just above his head. If that had made contact, he'd be nursing a concussion right now, so he decided it might be time to give his opponent a friendly warning.

'You might want to take it a little easy on me today, buddy. I have a city to run now, remember?' he quipped.

'Any excuse to try to win,' Ronon grunted, swinging his arm around and swiping his stick so it slapped Sheppard hard across the stomach.

The colonel sank to his knees in the middle of the sunburst pattern on the gym floor, clutching at his aching abdomen. 'No fair. I wasn't ready.'

'If I was the enemy, I wouldn't wait until I thought you were ready,' Ronan smirked, standing back and waiting for him to get up on his feet again.

'If you were the enemy, I'd have shot you by now,' Sheppard fired back, rising carefully and taking a few deep breaths to re-inflate his lungs.

They'd been sparring for no more than twenty minutes, but already he was feeling fatigued. He knew it would be down to the cumulative effect of his lack of sleep over the past six days, but he hated to admit he was below par. He raised his stick, ready to stave off Ronon's next assault.

'You been to see Elizabeth today?' the Satedan asked, out of the blue.

Sheppard dropped his arms to his side. 'Well, I watched her for a while this morning, but I'll probably visit her la –.'

As he spoke, Ronon swung his staff unexpectedly into the back of his calves, knocking his legs straight from under him. He thudded to the floor, the back of his skull making hard contact with the wooden surface and shaking his brain cells a little more than they were prepared to accommodate.

'You all right?' Ronon asked, still smirking.

For a moment or two, Sheppard kept his eyes closed, waiting for the throbbing to subside to a level where he thought it might be safe to let light back in again. When he did so, there were spots dancing in his vision.

'Thanks for going easy on me, Chewy!' he croaked, still not daring to move.

'If I don't push you, you'll get complacent,' Ronon grinned, reaching out his hand and tugging him back up to his feet.

'And if you push me too hard, I'll be in the infirmary,' Sheppard pointed out, swaying with the change in altitude. 'I'm beginning to think reading reports was the better option.'

'Your promotion's making you soft.'

Sheppard knew is friend was baiting him, but humoured him anyway. Ronon loved a good scrap and it was a great way to release his tension. It beat taking breakfast with a psychologist any day.

'Oh, you think so?' he asked, his face cracking into a smile. 'We'll see.'

He launched himself at Ronon, managing to catch his right arm with his staff. The Satedan sucked in a breath through his bared teeth, but it didn't slow him for long. He leapt into his trademark move, bringing his staff down toward Sheppard's shoulder. The colonel managed to block the shot, forcing Ronon back, then kicking him away with a foot to his stomach.

Ronon smiled, appreciative of his efforts. 'Maybe I was wrong,' he admitted, rushing at him again.

His sheer momentum almost bowled Sheppard over, and he had to take several hurried steps back to steady himself while Ronon span wildly, reining blow after blow on him, only some of which he got his staff in the way of. Eventually, Ronon span round behind him and cracked him across the shoulder blades, sending him spilling forward onto his knees again. His upper arms, ribs and shoulders throbbed, and he considered just staying put, but he forced himself back to his feet again and spun his staff in one hand with practiced skill. 'Okay, that was good...but I can still take you down whenever I want,' he challenged.

Ronon's grin grew fierce. 'Bring it on, Boss Man.'

Taking a deep breath, Sheppard tried to replicate Ronon's own style, spinning and clubbing for all he was worth. Unfortunately, Ronon anticipated each strike, blocking them one after another and biding his time until Sheppard was off balance, when he simply swiped his feet from under him.

Once again, Sheppard found himself staring up from the floor, his vision tilting erratically as his befuddled brain tried to make sense of his sudden change in position.

'Well, I may have been a little optimistic in my assessment,' he confessed, letting his head drop back to the floor.

'You give up?' Ronon asked, standing over him, spinning his staff as if waiting for the chance to whack him all over again.

Noticing his cheekbone stung, Sheppard reached up and touched tentatively at his face, finding it swollen and tender, the surface grazed and slightly bloody. He didn't even remember Ronon hitting him there, but things had got pretty wild so he wasn't surprised he'd missed it. 'Er...yeah. You win. Big surprise,' he grunted, sitting up and dabbing at his injury with the back of his hand.

'You all right?' Ronon asked, tossing him a towel.

'I will be,' he replied, gently pressing the cloth to his graze. When he pulled it away, there was a little blood, but not much. He guessed that meant it wasn't too bad.

'You should probably get that cleaned up.'

'Nah. It'll be fine,' the colonel assured him, pushing up to his feet.

'I might go check how Teyla is,' Ronon said, towelling himself off. 'She seemed pretty upset when she left your office.'

'I don't know. I think it might be better if we give her some space,' Sheppard suggested, feeling awkward as he remembered their disagreement. He'd really overstepped the mark with her, but hoped she just needed more time to get over it.

'You ready to tell me what you argued about?' Ronon asked him, heading over to one of the window seats and sitting down.

Deciding he needed a rest himself, Sheppard joined him, popping one leg up onto the seat and resting his elbow on his knee as he held the towel to his graze. 'I accused her of setting up a meeting between me and Dr Heightmeyer this morning, but apparently she had nothing to do with it.'

'You mean what happened at breakfast? I thought you decided to sit with her yourself.'

'No. I think it was what could be termed 'an ambush',' he replied, turning his gaze to the window. Once again, he felt compelled to check the sky as far as he could see, just to convince himself there was nothing untoward approaching them.

'So you thought Teyla had spoken to Heightmeyer and told her she was worried about you?'

'Yeah.'

'Well, she is worried about you, but I don't think she'd go to Heightmeyer behind your back.'

'No. That's pretty much what she said...with added volume and the tears.'

Ronon nodded, his expression unusually serious. 'She's feeling the strain herself right now. We all are.'

'I know. I doubt I would have turned on her the way I did if I weren't as worried about things as I am.' He looked at his friend now, wondering whether or not to put his next question to him. But he valued Ronon's opinion as a military man; he was a good judge of what was and wasn't dangerous. 'So, what do you think of all this business with Elizabeth?'

Ronon squinted at him. 'All what business?'

'Her abduction by the Asurans. Why, what did you think I meant?'

'Nothing,' the Satedan replied, his expression giving nothing away.

Sheppard wondered if McKay had let something slip from their interview with her the other day. It was bad enough that people at the SGC and the IOA were analysing what she'd meant, without everyone on Atlantis doing the same. 'So,' he said, continuing where he'd left off, 'what do you think?'

'I think what they did stinks – and so does the fact she's back on Atlantis.'

Sheppard frowned. 'What d'you mean?'

'Smells like a trap.'

Sheppard's heart sank. That meant his whole team was experiencing misgivings about Elizabeth's return. They couldn't all be wrong, could they?

'You think they tampered with her nanites?'

Ronon shrugged. 'Don't know much about how that stuff works, but I can't think of any other reason they would have left her somewhere for us to find.'

The two men held each other's gaze while Sheppard mulled over his friend's words. He certainly wasn't thinking anything he hadn't considered himself. He forced the other question that had been simmering at the back of his mind past his lips. 'Do you think she's consciously deceiving us?'

Ronon paused, then shook his head. 'I don't think so. All I know is there's trouble coming. I can feel it.'

'I know what you mean. I get up every morning wondering if today's the day the crap will hit the fan.'

'I wish I could say something to make you feel better, but I'm not much good at that stuff,' Ronon said, standing up. 'Everyone's on edge. I even saw McKay chatting to Heightmeyer this morning. I couldn't make up my mind which one to feel most sorry for.'

Sheppard laughed. 'Yeah. I know what you mean. But who counsels Heightmeyer after a session with Rodney?'

Ronon grinned, sauntering away to the door. 'Catch you later, buddy,' he called back as he exited, the door sliding shut behind him.

Sheppard sat still, feeling the aches in his body developing and throbbing to remind him he was alive and...well...still human. It made him wonder how Elizabeth felt, knowing how much damage she'd sustained, but not being able to feel any effects. It wasn't natural, and the fact the only thing holding her together were a few hundred minute robots had to be scary. It occurred to him then that Elizabeth might have suggested Heightmeyer speak to him if they had been in contact at all. He could well believe Elizabeth was concerned enough about him to think he needed to talk to someone. And she knew the pressures he was facing better than anyone...

Not wishing to repeat his mistake with Teyla, he decided to pay her a visit and allay any fears for his stability she might be harbouring. Was he feeling the pressure? Damn right he was, but he wasn't about to fold just yet. There was a lot more mileage left in him before he called it a day.

*****

Feeling a pang of guilt at the smile Elizabeth gave him when he stepped in through her door, Sheppard hung back several feet, pushing his hands into his pockets and avoiding her gaze like a naughty schoolboy.

'I wasn't expecting to see you just yet,' she said brightly. 'I thought I was an 'end of the day' project.'

'Well, I just checked in with Dr Keller for an update on your condition, and she said you were bored so I thought I'd see if I could help.'

'I see. So you thought gracing me with your sparkling personality would alleviate the tedium?' she asked with a smirk, peering up at him through her long lashes.

'Yeah, something like that,' he replied, feeling his cheeks burn. Somehow, knowing how she felt now made her flirting a little more difficult to deal with. He missed the uncomplicated chats they used to have, the ones where feelings were hidden and didn't get in the way to mess things up.

'Have you heard anything from the IOA about what they have planned for me?' she asked, her smile melting away.

'I have, but I'm not at liberty to tell you what they said,' he half apologised. 'Needless to say, it wasn't a straight forward chat; you know how much they like to discuss and analyse things.'

'That I do,' she nodded. 'In all honesty, I'm expecting them to tell you to shut down the nanites.'

He gazed into her huge green eyes seeing the pain that thought brought to her. 'I don't think it'll come to that, Elizabeth. They're not in the habit of handing out death sentences lightly.'

'I wish I shared your optimism, but considering the threat my nanites pose to everyone on Atlantis, they may have to make that call.'

'They'll find another way,' he promised her.

'What, like locking me away in an isolation cell for the rest of my natural life. I really don't see that as a better option.'

'Well, Rodney's working on something else – but I'm not at liberty to divulge the details of that, either,' he told her, hoping even that glimmer of hope would bring the smile back to her face.

She did smile, but it wasn't exactly brimming with happiness. 'Rodney can't fix everything, John. I think this little problem may be beyond even him.'

'Well, if he can't do it alone we can bring in help. Sam Carter has a lot of experience with Replicator technology. I bet if we put the two of them in a room to thrash this out they'd soon have it figured.'

'If Colonel Carter didn't kill him first. My understanding is the two of them don't often see eye to eye.'

'Well, no, I heard that, too. But I think they could keep this professional enough to solve your problem before they came to blows.'

'Hmmm, perhaps.'

John pulled up a chair and sat down across from her, maintaining just enough distance so that she couldn't touch him without getting out of her seat. 'This must all be very scary for you, Elizabeth. How're you coping?'

'Oh, I'm all right. I spoke with Dr Heightmeyer yesterday and got a lot of things off my chest. I'm feeling more relaxed now.'

So she had spoken to Heightmeyer. Now he suspected she had set the doctor on his tail. 'That's good. I'm glad it helped.'

'Yeah. I told her some things in confidence that I'd like her to share with people if I don't survive this, and she's promised to pass those messages on.'

'Now, don't talk like that. Everything's going to be fine,' he assured her.

'Well, it's nice that you want me to feel that way, but you'll excuse me if I don't completely share your optimism,' she sighed, pushing her hair behind her ear as she looked at him. 'It's time to start being realistic, John. There's a good chance I won't get through this, and you need to prepare yourself for that prospect.'

'I suppose you think I should see Heightmeyer and get some therapy,' he quipped, hoping to draw her out on the topic.

She frowned and shook her head. 'I don't see you as the therapy type. But you do have to get your head around the fact that this place needs a new leader. Perhaps you should apply for the permanent position.'

'Are you kidding? A couple of days of dealing with the IOA is enough for any sane man.'

She smirked now, trying hard not to laugh as she asked. 'What does that say about me?'

Sheppard sputtered a laugh out into his chest. 'That didn't sound quite the way I meant it to,' he confessed. 'You're the sanest person I know.'

'What? Even with these damned nanites in my head?' she asked. Then, she flinched, touching at her temple.

Sheppard felt his heart leap into his throat, certain this wasn't a good sign. 'Headache?'

She stared blankly ahead of her, focussing on nothing at all. Sheppard wanted to jump up and shake her, but couldn't. All he could do was raise his voice.

'Elizabeth!'

She remained in a trance for a few seconds longer before he repeated her name and she finally snapped back to him.

'Yes...sorry,' she apologised, still rubbing her head.

'Headache,' he asked again.

'Yeah – it's not bad. I'll just ask Keller for another mild painkiller and it'll soon be better.'

'You've had this before?' Angry that no one had told him about it, Sheppard glanced toward the door. 'Funny. Dr Keller never mentioned that.'

'Well, she should have. You should pick her up on it. Now you're in charge everyone should keep you apprised of everything, no matter how insignificant it seems,' she told him, still rubbing deep circles on her temple.

'I guess people are still getting used to my change in role. I'm sure she didn't mean to leave me out of the loop.'

'You look tired, John. If you have enough spare time to visit me, maybe you should be using it to get some rest,' she advised him. 'I might try to get some sleep myself.' She hopped up on the bed, her feet swinging as she looked at him with barely masked concern.

'You got any other symptoms I should know about before I go see Keller about those painkillers?' he asked.

'No, just that and the tiredness. She said it was probably just a side effect of having the nanites functioning in place of real tissue. Some kind of compatibility issue they're still fighting out in there.'

That didn't ring true to him. She'd been fine until today, not showing any sign of excessive tiredness at all, the exact opposite in fact. 'Well. She's the expert,' he muttered, pushing up out of the chair. 'I'll leave you to get some rest.'

'Thanks...and don't forget the Tylenol.'

'I won't,' he promised, heading out into the corridor. Once the door had closed, he asked the guards to be extra vigilant before heading off to find Keller.

The young doctor was working at her desk when he knocked on the doorframe and entered without waiting for an invitation. 'Why didn't you tell me about the headache?'

'Oh, Colonel...er, you mean Elizabeth's headache?'

He fought hard with the urge to roll his eyes. 'Yes, of course I mean Elizabeth's headache.'

'Well,' she said, standing up and nervously approaching him, 'It wasn't that bad and a dose of Tylenol soon sent it packing. It didn't seem important enough to bother you with.'

'Everything that happens to Elizabeth is important,' he snapped. Then, to avoid misinterpretation, he added, 'She has Replicator nanites in her brain. If she gets a headache, I need to know about it.'

'Of course. I didn't mean to keep it from you. Sorry.'

He saw she meant the apology sincerely, so calmed down before continuing. 'Did you find any cause for it?'

'Nothing,' she said, shaking her head as she picked up the data file from her desk and called up the relevant files. 'I ran several scans and the nanites are still acting in the way they always have been. No change.'

'So...it's just a headache. Possibly caused by stress?'

'I'd say there's a good chance that's the case. I certainly wouldn't want to be in her shoes right now. Or it could just be the fact that she has nanites in her brain instead of normal tissue. We've never done this procedure with anyone before, so it's hard to know what to expect, but I don't think it's out of the question that they might cause the odd ache or pain.'

'As long as that's all it is,' he said, feeling a wave of relief wash over him.

'There is one other possibility,' Keller said, looking sheepish. 'But I don't want to sound like the doomsayer here when it's probably nothing.'

That sense of relief was immediately gone. 'What?' he demanded.

'Well, it could quite plausibly be her immune system trying to reject the nanites. They are a foreign body after all. As yet, there's no other symptoms to suggest that's the case, but it's a definite possibility.'

He was no medical expert, but he knew that didn't sound good. 'Is that serious?'

'Normally, the body rejecting something that's been implanted to keep it alive would be disastrous. But when the thing keeping you alive is nanites...I don't think she'll come to any harm. They are programmed to keep her alive, after all.'

'Yeah...I suppose...' he mused, turning to face the feedback of the Isolation room playing out on a screen in her office. 'But I think it might be an idea to step things up a little until we know exactly what we're dealing with. I want someone watching feedback from her room around the clock, not just checking in on her every thirty minutes. And the first sign of any further problems, or anything unusual in her behaviour, I want to know about it. Okay?'

'Absolutely,' she nodded, wide-eyed and serious as he handed out his orders. 'I'll get that set up right away.

'Thanks. Oh, and Elizabeth has another headache. She's asking for painkillers and says she feels tired.'

'Really? Again? I think I'd better go examine her. Thanks for letting me know.'

'No problem. Oh, and just one other thing, you didn't discuss my lack of sleep with Dr Heightmeyer, did you?'

She shook her head, her mouth twisted down in thought. 'Nope. I really haven't had time to discuss anything with Kate for the past few days. We're treating so many people injured when the satellite weapon hit the city, and now with Elizabeth here, well...I'm having trouble finding time for sleep myself, to be honest.'

'You'd better make sure you take care of yourself, Doc. We can't afford to have the CMO fall ill, can we?'

'Don't worry. I'm not about to collapse just yet. I'd better get those pills to Elizabeth and check her out.' She squeezed his forearm as she passed him on her way to the medicine cabinets.

He turned and watched Elizabeth for a moment longer, thinking over the way her reappearance was affecting him and his connections with the rest of his team. Rodney was freaking at his friendliness, Teyla believed he'd lost trust in her, and Ronon thought he was going soft. As he thought about them all, the sudden realisation of just who had spoken to Heightmeyer on his behalf struck him. Then, he stormed out to tell the guilty party just what he thought of their interference.


	15. Chapter 15

Rodney was busy checking the new sample nanites when he heard the familiar sound of Sheppard's boots approaching his workstation.

Looking up, he briefly noted how pissed the colonel looked, but putting it down to lack of sleep he broke into conversation. 'Ahhh. Good timing. If you're here for another update on Elizabeth, I can tell you that as of this very moment, the nanites are still behaving within expected parameters.'

'That's good to hear,' Sheppard replied, planting his hands on his hips. 'But I—'

'Now, I'm not one to say I told you so, but I believe I did say I could make sure those nanites were entirely safe.'

'Yes, you did, McKay. But –'

'Oh,' Rodney interrupted, tapping away to bring up some other files. 'I found something fascinating today...and when I say I, it was actually Zelenka who discovered it when he was working on repairing the connection between the weapons system and the chair, but I figured out exactly what it did.'

He spun his laptop toward Sheppard, whose eyes darted across the screen, then lifted to his in confusion. 'What exactly am I looking at?'

_I thought this guy was supposed to be MENSA, _Rodney thought, biting back a stream of barbed comments. 'It's a remote link between the chair and the jumpers.'

'Remote? What do you mean?' the colonel asked, his interest clearly piqued.

'I mean it facilitates the act of flying a jumper via the control chair. All you have to do is think it up into the sky, and there it goes.' He made a little upward soaring motion with his hand as if that would clarify things for the pilot far more than words could.

He watched as the annoyance marring Sheppard's expression slid from his face to be replaced by mild excitement. 'So someone can just go sit in the chair and send up a few jumpers?'

'Well, theoretically...' Rodney replied, scratching his hair. 'Of course, I have to activate the correct component in the jumpers to allow them to be controlled that way. And whoever sits in the chair has to have the ATA gene, and would preferably be a pilot, but that goes without saying. Apparently the Ancients used the facility to send out decoy ships if anyone got too close to the cloaked city. That way, they didn't have to lose personnel if it turned out they were aggressive.'

'Clever,' Sheppard said, nodding appreciatively. 'That could certainly come in useful some time. Can you get the jumpers activated to accept the remote commands?'

'Well, yes. Of course. And whereabouts on my list of jobs that should have been done yesterday should that go?' he snapped, watching Sheppard's scowl return.

'I told you to delegate, McKay,' he growled, folding his arms across his chest and standing firm in the face of what McKay could feel to be one of his rants building.

'I am delegating, but there are only twenty-four hours in the day if you hadn't noticed, and I'm already working twenty of them even after I've shared stuff out.'

'All right. Then, at the risk of annoying you further, have you had time to look into making the Replicator disruption weapon?'

'Ahhh, now that one I could delegate,' McKay grinned, grabbing his tablet and flashing it toward his friend. 'I've written a program that will, based on the information we've been able to gather from Elizabeth's nanites, extrapolate a frequency that should disrupt the bonds between the Replicator units should they spread. I can just sit back and let it run knowing it's in safe hands.' As if to demonstrate, he leaned back in his seat, knitting his fingers behind his head as he smirked at the colonel.

'Except, of course, you have some jumpers to align to the control chair,' Sheppard reminded him. 'And I'd still like you to figure out a way to get those nanites to fix Elizabeth up so we can shut them down.'

'Well, I was relaxed for...what was that...all of ten seconds?' McKay sniped.

'This isn't a holiday camp, McKay. I need everyone working to their full potential.'

'My team are working to their full potential and way beyond. I can't ask them for any more than they're already giving,' Rodney whined. Sometimes, having Sheppard think he was some kind of god was too much even for him to handle.

'Okay...you're right. We don't want anyone else getting sick. Looks like we should've kept the Daedalus around a while longer. I'm pretty sure the crew could have helped you out.'

The suggestion he couldn't get things up and running without SGC help soon had him on the defensive. 'Well, we weren't to know things would start breaking down after they left. And they have other duties to carry out. Anyway, I'm confident we'll have things back up and running in a couple more days.'

He watched Sheppard nodding, but sensed the man was still troubled by the holes in their defences.

'Just get me one jumper operating from the control chair, Rodney. D'you think you can manage that?' Sheppard asked.

'I could probably find time to fix one up, yes. But I doubt one jumper is going to provide an effective defence against the Replicators if they turn up.'

'It might create a diversion to buy us the extra time we need. Anyway, you leave worrying about defending this place to me, Rodney. You just need to focus on fixing things.'

McKay nodded grimly, the good humour the discovery with the control chair had brought now completely dissipated. 'Have you seen Elizabeth today?' he asked, unable to hold Sheppard's gaze when the colonel lifted his eyes to meet his.

'Yeah. She has a headache – second one she's had in twelve hours. I've asked the medical team to keep a twenty-four hour watch over her via feedback from the isolation room, and I've told Keller I want to know the minute she spots any kind of change.'

'Headaches? Huh,' Rodney mused, thinking that through. Although any symptom had to be checked out, he suspected Sheppard was being overly cautious in his approach. 'I'm sure she'll be fine. I think if I had that many nanites holding my brain together, I might get the occasional headache, too.'

'Yeah...hopefully, that's all there is to it,' Sheppard replied. 'Are you ready to update the IOA on the nanite situation?'

'Yes. I've prepared a file for them, and I plan to give them a quick reprise to ensure they understand the data. Are you going to sit in on it?'

Sheppard grimaced at the mere thought of it. 'No. You can technobabble to your heart's content, Rodney. I trust you to tell them what they need to know.'

'I do not 'technobabble'! Babbling suggests the use of more words than are entirely necessary.'

Sheppard just raised his eyebrows and Rodney immediately admitted defeat. 'Fine. Have it your way. So, just to clarify, fixing the control chair, sorting out the hyperdrive, extending the shield, setting up a jumper with remote access, recalibrating the Replicator disruptor, and fixing Elizabeth's nanites are my priorities, right?'

Sheppard nodded. 'Sounds right. Oh, and Rodney...one more thing...'

McKay rolled his eyes. He couldn't seriously be about to give him more work. 'What!'

'If you talk to Heightmeyer about my ability to cope behind my back again, I'll kick your ass into next week. Understood?'

His throat suddenly dry, Rodney forced down a nervous swallow. 'Y...you know about that?'

'It wasn't exactly subtle, Rodney. Now, maybe you did it out of genuine concern...I'm willing to give you the benefit of the doubt on that...but it doesn't happen again. Is that clear?'

'Yes...yes...I'm sorry. I was only trying to help.' The words tumbled out of his mouth as he saw the real anger in his friend's expression. He and John had already almost come to blows recently; he didn't think it would be wise to push him any further.

'I'll swing by for an update in a couple of hours,' Sheppard said, turning quickly and striding away, his hunched shoulders and tense demeanour now making complete sense.

Rodney was left wondering if approaching Heightmeyer with his concerns had been the right thing to do after all. Sheppard clearly wasn't doing so well; was he the only one who could see that?'

oooOOOooo

Sitting in the pilot seat of Jumper One, his tablet plugged into the flight controls, Rodney opened up the relevant systems to allow for remote flight from the city's control chair. It wasn't turning out to be as easy as he'd hoped, leaving him wondering why the Ancients seemed to do everything in the most complicated way possible. Unless, of course, none of this was complicated to them. He pondered that for a moment, before shaking the thought away. There was no way anyone was that much smarter than him, no matter how advanced their civilisation was.

Though he heard a shuffling sound behind him, he didn't bother turning to find out who was there as he was pretty certain he already knew.

'Rodney. Is that you?' he heard a gentle Czech voice ask.

'Yes, yes. Who else would it be?' he huffed, continuing to work without looking up.

'I thought you had things to do in the lab.'

'Yeah...you and me both.'

Radek hesitated before continuing. 'Is this to do with those remote systems we found for controlling the jumpers?'

'Yes, what else?'

'Are you sure there aren't more important things you should be working on?'

With a sigh, McKay slapped the tablet down onto his lap. 'You would think so, wouldn't you? But Colonel Sheppard has asked me to get one jumper connected to the control chair, so...here I am.'

Radek looked decidedly confused, his brow furrowing as he thought about what Rodney had said. 'Colonel Sheppard asked you to do this?'

'That's right. Honestly, if he wants to play with toys I'll buy him an RC car for Christmas. This is a ridiculous time to be working on this!'

'Well,' Radek countered thoughtfully, 'if Colonel Sheppard thinks you should fix it now, he must have a good reason.'

'Oh, you think so? Well, I can't think of one, can you?'

Radek shrugged, pushing his glasses up on the bridge of his nose. 'I don't have the kind of strategic sense Colonel Sheppard has. I'm sure he has a good idea of what he's doing.'

'Do you? Well, you'd better hope so, because if he's cracking under the weight of his position, we're all going down with him.'

Rodney saw the look of barely contained horror creep onto Radek's face and felt a little guilty about his outburst – not that he was going to back down.

'Is that what you really think?' Radek asked.

'Well, he's never wanted to run this place. He should hand the reins over to someone who wants them.'

'And by that you mean someone like you, I suppose,' Zelenka said, quirking an eyebrow.

'Well, Atlantis could do worse.'

Radek muttered something that sounded remarkably like '_And they could do a lot better, too_,' but Rodney chose to ignore it. 'I still think Colonel Sheppard is the best person for the job right now,' the Czech said, this time loud enough for McKay to be sure of what he said.

'He doesn't even want the job. The IOA should pick someone else to lead the expedition and get it over with. And let's face it – who's saved our asses more times than anyone can remember?'

'Err...Colonel Sheppard?' Radek suggested, wincing even before McKay could erupt.

'Me, Zelenka. I've saved us countless times. Every time there's a scientific problem, who does everyone turn to...me!'

'Well, yes...that's true. And you are definitely the person to call on in a scientific crisis, but leading Atlantis requires more than just academic intelligence.'

'Such as?'

'A level head, the ability to negotiate, diplomacy, people skills...'

'I have all those things,' McKay snapped.

Radek peered at him over the top of his glasses, looking doubtful.

'What, so you think Sheppard is better at all those things than I am?'

Scratching his head, Radek shrugged his shoulders again. 'Well...yes...actually.'

'That is so like you! I suppose you think threatening to kick my ass into next week is 'diplomatic', do you?'

'What did you do to upset him, Rodney?' his Czech friend asked wearily.

'Oh that's right, blame me. You are such a suck up, Radek!'

'What did you do, Rodney?' Radek repeated, folding his arms and fixing him with a disappointed stare.

'Well...I may have told Heightmeyer I thought he was struggling to cope,' Rodney confessed, pulling his collar away from his hot neck. 'And that she might need to do an assessment.'

'Then I'm not surprised he's mad with you. You had no right.'

'No right. The whole station is in his hands and he's freaking out over a friend showing a little concern!'

'He's a private man, just as you are, Rodney. How would you feel if someone had done that to you?'

Rodney hated it when Radek was right. It didn't happen often, because the man suffered from a hugely inferior intellect, but every now and again he made a valid point that forced Rodney to rethink his position on things. 'Well, that's beside the point. Now, if you'll excuse me, I have to finish this up and then report to the IOA regarding the condition of Elizabeth's nanites. Off you go!' He clicked his fingers, then flicked his wrist to gesture toward the rear hatch.

Zelenka scowled, shuffling away. 'Tebe arogantní polda!'

'One of these days I'm gonna learn Russian and then I'll know exactly what you're saying,' Rodney called after him, annoyed that he couldn't understand Zelenka's insults.

'I'm from Czech Republic, Rodney,' Zelenka grunted.

'So you don't speak Russian there? How am I supposed to know that? I never claimed to be an expert in linguistics, did I?'

'Hlupák blbec,' the Czech spat back at him, leaving before he could be drawn any further on that.

'Huh! Wonder what's eating him?'Rodney muttered to himself, picking up his tablet and continuing with his work. With only two hours left before he needed to update the IOA, he couldn't afford to waste any more time trying to work it out.

'Thank you for agreeing to feed back to us, Dr McKay. We appreciate your input in this serious matter.'

'Well, you know me. Always happy to help,' McKay said, giving Mr Woolsey a lop-sided smile via the video link.

'Yes...quite. So what can you tell us about Dr Weir's condition?'

'Well, I'm not really qualified to comment on her medical condition, but if you want to know what's happening with the nanites, they're behaving just the way I programmed them to.'

'That's good to hear, Dr McKay. And you're monitoring them on a regular basis, I presume.'

'Every half an hour,' he said, throwing the bespectacled bureaucrat a self-satisfied smirk.

'Very good. And how does Dr Weir seem to you, Doctor?'

That flustered him a little. In truth he hadn't been back to see her in person since her slip-up in the interview with Sheppard. He didn't handle things like that very well, so it was easier just to avoid the chance of any awkward questions she might pose about the colonel. 'Well, as you can imagine, my team and I have been tied up with all the repairs Atlantis needs, so I haven't had a chance to visit her in the last twenty-four hours. However, I did speak with Colonel Sheppard a short while ago, and he told me she was experiencing a few headaches, so he's asked the medical team to keep a round the clock vigil via the live feedback.'

Woolsey nodded appreciatively. 'That would seem a wise move under the circumstances.'

Rodney thought about it. Although he'd considered it somewhat of a knee-jerk reaction at the time, he supposed he could see the sense in it. Although the headaches alone weren't anything serious, if the symptoms changed, they might prove to be relevant in making a diagnosis. 'Yes, I agree. Colonel Sheppard certainly seems to have a good handle on the situation.'

'That's good to hear, Dr McKay. I was wondering if you'd mind giving me your assessment of how Colonel Sheppard has performed his duty over the past several days since Dr Weir's unfortunate accident.'

For once, McKay picked up on an undercurrent. They wanted him to tell them Sheppard wasn't coping. He supposed it was no surprise; despite the fact Sheppard had, time and time again, saved the Atlantis expedition from certain doom – oh, God. Zelenka had been right about that – the IOA and the SGC saw him as something of a loose cannon because of his propensity to break the rules. Well, maybe they did want to shoot Sheppard down, but they weren't going to get the ammunition with which to do it from him. The colonel _was_ doing a good job; he could see that now.

'I think everyone here would agree he's coping admirably under exceptionally difficult circumstances,' he assured Woolsey.

'Yes, but I'm sure he's finding the situation with Dr Weir particularly...distracting.'

Though he knew exactly what Woolsey was hinting at, once again, Rodney leapt to the defence of his friend. 'We all are. Elizabeth has been a great leader and a good friend over the years. None of us want anything bad to happen to her. In fact, I'm currently working on re-writing the nanite programming to get them to repair Elizabeth's tissue itself – it was Colonel Sheppard's idea. He wants to neutralise the threat completely by shutting them down.'

'Yes, Colonel Sheppard told us about that this morning. It certainly would seem the best way to deal with them. And do you believe you are able to do that, Doctor?' Woolsey asked, leaning forward with his increased interest.

'Well, I'm not going to pretend it'll be easy, but gimme a couple of weeks and I should have it done. Soon, Dr Weir will be one hundred percent organic again.'

'I imagine that would be a relief for everyone involved there...particularly Dr Weir. I would be very grateful if you could keep us apprised of your progress.'

'Certainly,' Rodney smirked. 'I'll schedule it in between the one hundred and one other jobs I have to do.'

Woolsey looked mildly annoyed, but kept his tone civilised. 'I appreciate you're a very busy man, Dr McKay, but I'm sure you understand the importance of keeping everyone here up to date on what's happening on Atlantis. We want to offer all the assistance we can in this difficult time.'

'Of course,' McKay sneered, wondering why, if that was the case, they hadn't asked Sam Carter to return. But he was a proud man; he wasn't about to suggest they send her in. He would figure it out eventually. 'There's no need for you to worry. We have everything under control here.'

'I'm very glad to hear that. We look forward to analysing your datafile. Now, I won't keep you any longer since you're obviously in demand. Could you tell Colonel Sheppard that we'll discuss the matter further with him in our scheduled update tomorrow morning?'

_What am I, an errand boy? _Rodney thought, but what he said was something quite different. 'Of course, Mr Woolsey. I'll make sure he gets the message as soon as I leave here. Would you like me to give you a rundown of what's in the file I sent you before I go? '

'No, that won't be necessary. We'll have our experts take a look at it. They're familiar with Replicator tech so I imagine they will have no difficulty unravelling it all.'

Feeling somewhat rejected, Rodney floundered for a response. 'Oh...right. Well, if you do need any explanations, you know where you can reach me.'

'We do indeed.' Woolsey forced on a smile and a moment later the screen went dark. McKay sat back and breathed a sigh of relief. Maybe leadership wasn't as simple as he'd thought. No wonder Sheppard was keen to pass the torch to someone else. Dealing with bureaucrats was like treading on eggshells, and neither of them were very good at it, although, he reluctantly admitted to himself, Sheppard did seem able to practice more self-restraint than he did.

Checking his watch, he realised there was still an hour before the dinner break he'd built into his crazy schedule. His stomach complained, so he pulled out a power bar and chomped down on it, hoping it would tide him over well enough to prevent him going into hypoglycaemic shock.

All this stress was far too hard on his metabolism; maybe being the resident genius was as much pressure as he needed.


	16. Chapter 16

_**AN: After today's post I will be away on holiday until next Monday, but I will resume posting then. Thanks to everyone who has been reading and reviewing so far. It's much appreciated. :D**_

_Sheppard rolled onto his side and pulled his covers up, desperately trying to get back to sleep. He still felt exhausted and didn't even want to check his watch to see what time it was. His body was telling him to stay put, and he meant to listen to it this time._

_The sound of the ocean accompanied him through the window he'd left slightly open. The waves and the fresh air usually helped to lull him, but right now he felt so knotted up inside he couldn't relax. But why was he so worried; he tried to think about what was concerning him, but it wouldn't come into focus._

_He heard a voice calling his name, distant through his thoughts. It confused him for a moment, but then he realised someone was contacting him through his earpiece. He checked his watch, 0524 hours, and activated the link._

'_This is Sheppard.'_

'_Colonel Sheppard. Elizabeth's condition has deteriorated considerably. She's losing the fight. Yeh need to get down here right away, lad.'_

_The alarm in Carson's voice had him immediately leaping out of bed, pulling on his trousers and boots and running for the infirmary. The deserted corridors seemed longer than normal as he sped down them, as if they were trying to sabotage his attempts to reach his friend in time. Eventually, he made it to a transporter that took him to the infirmary level, almost directly outside the entrance. When he strode in, Carson, in full hazmat gear, was there to meet him._

'_It's not good, Colonel. The nanites are spreading throughout her body, taking over all her functions. There's a particularly high proportion of them in her brain and I believe they are trying to take command of her body. If we don't find a way to stop them soon, she'll become some kind of organic replicator and she'll turn on us.'_

'_Can I see her?' _

'_Of course, but you'll need to stay outside the isolation tent we've set up around her, son. We can't risk yeh getting contaminated, too.'_

_John nodded his understanding and followed Carson through to the room where Elizabeth was being treated. McKay was already there, studying a datafile. Though he couldn't see her clearly through the sheeting, Sheppard could make out she had her eyes closed. Carson started up the scanner and captured the latest images of her body's fight with the nanites. She was riddled with them._

'_D'you think she's aware we're here?' Sheppard asked, watching her untroubled exterior, in complete contrast to the fight for survival she was engaged in._

'_How can she be? She's unconscious,' McKay snorted._

_Carson joined John to look at his patient. 'Yeh may be right. Yeh could try talking to her – tell her to keep fighting.' _

'_And that will help exactly how?' McKay sneered, clearly not convinced by the doctor's suggestion. _

'_In a coma, one's sense of hearing is the last thing to go and the first thing to return. There are many cases where patients were actually able to hear others talking to them in their rooms,' Beckett explained patiently as if speaking to a petulant child._

_Rodney gave his a sceptical glare. 'And were these comas also caused by nanites invading people's bodies, hmm?' _

'_No, Rodney, but there are indications that she's thinking.' _

'_You mean dreaming?' Sheppard asked, wondering what kind of nightmares nanites might bring with them. _

'_More than that,' Carson replied. 'Her mind is extremely active for someone in a coma. Her EEG reads almost as if she were going about her daily life, which suggests she may well be able to hear us.' _

_Sheppard looked down at Elizabeth again. 'What the hell are they doing to her?' _

'_I wish I knew,' Carson confessed sadly. 'The immune-boosting drugs are having no effect.' _

_Sheppard felt anger at the lack of control they had over this situation rising inside him. 'Aggressive little bastards,' he muttered through clenched teeth._

_Suddenly, he heard McKay snap, 'What?' _

'_What?' Beckett retaliated. _

'_Well, it's that look. That's the same look I get when I have a brilliant idea.' _

_Thinking that and odd thing to say, Sheppard asked, 'How would you know how you looked?' _

'_Cause it's happened more than once in front of a mirror, okay?' McKay explained. Then he turned back to the doctor. 'Carson, what is it?' _

'_I don't know about brilliant, but it just might...Excuse me,' was the enigmatic response as he hurried away. _

'_What are you doing?' McKay called after him, heading in the same direction. _

_That left Sheppard alone with Elizabeth. He struggled to come up with the words he wanted to say. 'You know, if Carson's right and you can hear me, I suppose I should say something profound.' He paused, trying to think of something, anything that might help her. Nothing came to mind. 'OK, I'm not so good at profound,' he admitted, 'but you should know we're doing everything we can to get you through this. These, these nanites, I don't know what they're putting you through, I don't know what they're doing to you, but...don't let 'em get to you.' _

_He saw a flicker of movement behind Elizabeth's eyelids, showing signs of her brain's continued activity._

'_We're doing everything we can to bring you back, but you've got to do your part. You've got to fight this.' _

_He continued to talk to her that way, urging her to fight, telling her to stay with them, to try to wake up and come back to them, and although he could see how busy her mind was, she just couldn't do what he asked. Teyla and Ronon now joined him, too, Teyla doing her bit, though Ronon looked visibly uncomfortable with the thought of talking to the unconscious woman. Nothing they said made a difference. His friend was dying in front of him and there wasn't a damned thing Sheppard could do to stop it._

_As he battled to keep down his surging emotions, Carson and Rodney returned._

'_Okay. We think we've found a way to uncouple the nanite cells from Elizabeth's cells,' McKay announced. _

'_We?' Beckett repeated in a tone that suggested he had done most of the work. John really didn't care who was responsible, he just wanted to know what they planned to do. _

'_How?' he heard Teyla asked before he had the chance to voice the question himself._

'_We create a distraction,' Rodney told her. He held up a small cylinder, smiling smugly. _

_Carson took it from him and carefully put it down on a nearby trolley, as if he thought it might explode if he left it in Rodney's hand any longer. 'It finally occurred to me why I wasn't having any success...' _

'_What were the nanites originally designed to do?' McKay blurted out, interrupting him. _

'_Fight the Wraith,' Ronon rumbled, his arms folded over his broad chest. _

'_Exactly,' Rodney grinned. 'So that's what we'll get them to do now.' _

'_We think by implanting a small amount of Wraith tissue into Doctor Weir's body...' Carson said, trying to pick up the conversation again. _

'_It's like a tumour,' Rodney added, interrupting once more._

'_Aye, a small tumour, yes – the nanite cells will essentially...' _

'_...attack it. They have to – it's what they are programmed to do, which will draw them away from Elizabeth's cells, effectively unbinding them,' Rodney said triumphantly._

_Tempering his enthusiasm, Beckett stepped in again. 'It will only last a few seconds or so, mind you, before the nanites attack the Wraith tissue and return their focus to Doctor Weir's cells.' _

'_Yeah, but that's all we need; momentary distraction to draw them away from her so we can zap 'em with the EM pulse.'_

_Sheppard looked back and forth between the two men, suddenly experiencing the weirdest sense of déjà vu. 'Wait a minute, wait a minute. This is all wrong. We've already done all this.'_

_His companions looked at him oddly, their expressions varying between amusement, concern, and contempt._

'_This is hardly a time for jokes, Sheppard!' McKay snapped. 'We need to do this if you want to save Elizabeth.'_

'_No...no...there's no point. This has already happened.'_

'_What do you mean, Colonel? Are you not feeling well?' Teyla asked, her brow puckering with worry._

'_I mean, we have all been through this. This is where it started...when we first realised Elizabeth had been infected with Niam's nanites. She got through this. We put the Wraith tissue into her, the nanites went for it, we blasted them with an EM pulse directed through the scanner, but some nanites survived and Elizabeth had to shut them down herself.'_

'_How did you know we were thinking of directing the pulse through the scanner? I hadn't even told you that yet,' Rodney gasped._

'_Because this has already happened!' he shouted, scraping his hands back through his black locks. 'Don't any of you remember?'_

_They were all still casting him dubious looks when another realisation struck him. He slowly slid his eyes in Carson's direction._

'_Aye, lad. You're right. I shouldn't be here.'_

'_You died. An explosive tumour took you out.'_

_Carson nodded. 'That's true, son. Only a few months after all this happened.'_

_The others still looked as baffled as ever, but Carson smiled at him, his kind eyes twinkling in the dim light of the lab. _

'_Am I dreaming this, because I have been having some seriously weird nightmares lately,' Sheppard asked him._

_Carson slipped off the helmet of his hazmat suit. 'You're asleep, but whether or not this is just a dream or something more significant...well...only you can make that decision.'_

_While he tried to fathom Carson's cryptic clues, he turned to look at Elizabeth. 'The nanites are dangerous, aren't they?'_

'_Yeh don't need me to tell yeh the answer to that, son,' Carson replied, stepping up to his shoulder._

'_Erm, excuse me. Shouldn't we be getting on with the procedure? Remember the nanites about to completely take over Elizabeth's body, anyone?' Rodney called from behind them._

'_This is significant in some way. Are the nanites really about to take over her again?' Sheppard asked the doctor._

'_Only time will tell. But yeh know in yer heart that something's wrong, don't yeh, son?' _

_He nodded, chewing his lip. 'So what do we do?' Can I use the solution you came up with?'_

_Carson shrugged, looking up at him with his clear, blue eyes. 'I'm not sure, John. It all depends on how far the nanites are spread, and whether the person inside really wants the little buggers to shutdown.'_

'_What the hell are you two gibbering about?' McKay demanded, turning Carson around to face him. 'We need to fix this. Now!'_

_Sheppard wasn't sure what happened next; he felt a crippling pain across the back of his neck and for a second or two, his vision blacked out. When he came to his senses, he was on the floor and he could hear shouting, panic, and equipment smashing. _

_He looked around for the cause of the commotion, spotting Elizabeth now on her feet with Teyla in a strangle hold while Ronon desperately tried to pull her off. _

'_Sheppard! Help me!' he screamed, and Sheppard was straight on his feet, swinging his full body weight off Elizabeth's right arm. It made not the slightest difference. He watched as Elizabeth choked the life out of Teyla, even as Ronon took a step back and fired shot after shot into her back with his energy weapon. She only let go when it was clear Teyla was gone. Without missing a beat, she shook Sheppard free, throwing him across the lab, then smashed her fist down on Ronon's weapon arm so hard the colonel literally heard the bone splinter._

_The Satedan crumpled to the floor, screaming in agony. Sheppard cursed himself for not bringing his gun, even though he knew it wouldn't have made any lasting impact. Though winded, Sheppard staggered back to his feet to put himself in her path again, determined to protect the others and desperately trying not to look at Teyla's lifeless body lying discarded on the floor. Elizabeth barely shook as he swung a right hook at her, simply returning the favour and sending him flying across the lab and into a bank of computers._

_As his blurred vision began to clear, he saw her advance on Carson, but as she reached him she stopped, frowning._

'_Sorry, love. I'm dead. There's not much yeh can do ta me.'_

_She accepted that without question, turning instead to Rodney cowering beside him. 'Please...God, no!'_

_She thrust out her hand, but unlike that of a true Replicator, it didn't slide through his forehead with ease, instead splitting his skull with a nauseating crunch. Sheppard froze in horror as she held McKay suspended like that for a few seconds longer, then snatched her hand back, leaving him to drop like a severed marionette. He folded, blood oozing from his injury, his eyes glazed in death. _

'_Carson! Is this what's coming?' Sheppard yelled to him, watching Elizabeth turn his way._

'_Possibly. Trust yer instincts, lad. They've never guided yeh badly before.'_

_Elizabeth was over him now, her eyes burning with the same anger he'd seen in Oberoth's eyes when he'd looked at him. 'You can't stop us. We are superior in every way.'_

'_I will stop you,' he vowed, listening to Ronon's growls behind him as he forced himself to his feet to try to defend his friend. Sheppard knew the Satedan couldn't help him, but he didn't care. This was a dream...there was still time to stop the nanites...to save Elizabeth._

'_Good luck, son,' Carson said, fading into the gloom of the failing lab._

_Sheppard fixed his eyes on Elizabeth's, and instead of being afraid, he smiled up at her. 'I'll save you,' he promised. _

_She frowned, then smirked. 'Only if someone saves you first.'_

_He closed his eyes as her hand came toward his forehead..._

At the first sensation of the impact, Sheppard's eyes snapped open. He was in his office – Elizabeth's office – feet up on the desk watching the feedback from the isolation room and had somehow managed to fall asleep again. He dropped his feet to the floor and leaned toward the screen. Elizabeth was rubbing her temples and a light sheen of perspiration glowed on her skin. She looked like she might have a fever. But weren't the nanites supposed to cure those kinds of things?

He tapped his earpiece. 'Sheppard to Keller.'

'Yes, Colonel,' she immediately responded.

'Any change in Elizabeth's condition.'

'_I was about to update you, Colonel. She seems to have developed a temperature, nothing too serious right now, but we plan to monitor her more closely. We've just carried out another scan and the nanites are still exactly as they should be, so this appears to be unrelated at this time. I'll do some blood work and see if I can figure out what's going on.'_

'But I thought the nanites should keep her well.'

'_Well, they were programmed specifically to fix life threatening injuries such as the one's she'd sustained after the satellite beam struck the city. It's possible they may overlook something as innocuous as a virus as long as Elizabeth's body seems able to fight it.'_

Sheppard scratched his hair, suppressing a yawn, 'So what you're saying is you think this may be a cold?'

'_It's quite possible that's all it is, yes.'_

Sheppard knew the young doctor might be well right, but his instincts were telling him there was more to it. Hadn't Carson told him to trust his instincts? Of course, Carson had been dead for weeks now, so the fact he was even considering taking his advice above and beyond that of a living doctor suggested his mental state wasn't quite as peachy as he'd hoped.

But, as he watched Elizabeth, a growing sense of foreboding stirred within him. He trusted her, but he couldn't say the same thing for those damned nanites lurking inside her. For now, he decided to bide his time. He wasn't ready to tell anyone about his freaky dreams just yet. Instead he chose to sit tight and hope they were nothing more than that.


	17. Chapter 17

Teyla made her way to the infirmary through bustling corridors, hoping she wouldn't find Sheppard there as she wasn't yet ready to face him. Quickly surveying the area, she realised he wasn't around, so made her way further into the room, seeking out Dr Keller. She found her checking one of her patient's medical records while adjusting their saline drip.

When she saw Teyla approaching, the doctor gave her a warm smile. 'Hi, Teyla. Here to check up on Elizabeth?' she asked.

'Yes...How is everyone here faring?' Teyla asked, looking around at the various occupied beds. Many of the patients bore minor cuts across their faces, but had been closer to the exploding window of the control tower than she, Rodney and Ronon had been, and so had suffered other more serious injuries as well – some internal traumas from the force of the blast, while others had eye injuries from flying glass that had required surgery to save their sight.

'Well, everyone's going to make it, but I can't guarantee a return to full health for all of them,' Keller said quietly, laying her hand on Teyla's back and steering her away from the main ward. 'Only time will tell.'

'And Elizabeth?'

Keller's smile grew more forced than usual. Teyla could immediately see the difference in her and it made her stomach sink. 'Well, she's a little unwell, but nothing serious,' the doctor admitted.

'How so?'

'At the moment, all signs suggest a simple virus, perhaps a cold or influenza. I'm just about to take her a dose of Oseltamivir to relieve some of the symptoms. But other than that, there isn't much I can do.'

'Could I take it to her?' Teyla offered. 'I would like to speak with her before she goes to sleep.'

'Er, of course. I'm sure she'll be glad of the company. You know where the suits are.'

Teyla considered it for a moment, but decided against collecting one. 'I might not wear one this time. I don't intend to go in there for long and since the nanites aren't spreading at all, I assume there's no risk.'

'No, none that I know of. In fact, I'm thinking of suggesting we lift the imposed isolation soon. I think the loneliness is really getting to her. With so much to do around Atlantis, people can't spare much time to sit with her. It's odd, but sometimes when I go in there, she barely speaks to me. I hope she doesn't blame me for all this.'

'I am sure that is not the case. I have been very lax with visiting her myself the past few days. I will be a better friend to her from now on.'

Keller gave her a sympathetic smile. 'Don't beat yourself up about it. There's a lot going on around here at the moment. Well, I'll get you the meds she needs and you can give them to her for me. I have to admit, there are other things I need to catch up on, so not having to stay with her will be a blessing this time.'

'I'll come back to you and let you know how she is doing,' Teyla promised, following her to the medicine cabinet.

'Well, you can if you want to, but there's no need. Colonel Sheppard has already insisted that we watch her round the clock, so we'll pick up anything we need to know about her condition from the surveillance cameras.'

Teyla was shocked at the news. No doubt if she hadn't spent the day avoiding him she would have know the colonel had ordered that, but even so, she was surprised he'd taken such action. It suggested he didn't trust Elizabeth, and John was always the one to give people the benefit of the doubt. 'Why has he ordered this?' she asked.

'Because of the illness. I think he's worried it's a symptom of something more sinister, but all signs seem to be saying it's all quite innocuous. I wouldn't let you in there if I thought any differently.'

'I'm sure you wouldn't, Doctor,' Teyla said, forcing on a smile. 'Colonel Sheppard is very protective of Elizabeth since her return. I'm sure he just wants the best of care for her.'

'Well, I won't argue with that. We all want her to get through this, and hopefully with some way for us to return her to normal.'

She handed Teyla the tiny plastic cup containing two tablets, then squeezed her shoulder and walked away. Teyla pondered her last words for a while longer, feeling guilty that she had to question whether she really did want Elizabeth to emerge from this unscathed. Yes, of course she did. No matter what it meant for her relationship with John, she wanted her friend to live. No one deserved to lose their mind to an occupying entity.

She hurried down the corridor to the isolation room, where one of the two marines posted outside activated the door for her. Inside, the room was darker than the last time she'd been there, the lighting subdued to ease the ache in Elizabeth's head, she assumed. The grey walls and dim lighting made the room feel even more cramped and oppressive than it actually was; Teyla couldn't help but be grateful she wasn't the one locked up in there. It was enough to sap the spirit from even the most positive of souls.

Elizabeth lay in her bed looking pale and tired, but perked up the moment she saw Teyla. 'Oh, at last. Someone who isn't going to turn me into a pin cushion,' she said, sitting up and hugging her bent knees to her chest.

'And I come bearing gifts,' Teyla quipped, holding up the medication for Elizabeth to see.

The relief was plain in her expression. 'Oh good, I was hoping it was that time again.'

Teyla set the plastic cup down on the stand beside Elizabeth's bed and backed off so she could pick them up. 'How are you feeling?'

Elizabeth tossed back the tablets, then took a drink from the glass of water also standing beside her bed. Teyla noticed that the jug next to the glass was empty, and made a mental note to take it to be refilled when she left. 'In all honesty...like a truck hit me,' Elizabeth replied. 'Dr Keller thinks I may have influenza. All I know is it feels like there are several bass drums pounding in my head most of the time. That's making it difficult to sleep, so...'

'I'm sorry to hear that, though relieved your sickness can be explained so easily,' Teyla said, affecting her most soothing tone.

Elizabeth nodded, leaning back against her pillows and laying her palm across her forehead. 'I know what you mean. I was terrified it might mean something far worse, so on this occasion, influenza is a welcome reprieve.'

Teyla pulled up a seat, though not too close, and sat down, letting Elizabeth know she intended to stay for a while.

Weir looked across at her. 'So, you choose today as the time to come in here without the hazmat suit? That's brave considering the germs flying around in this room.'

'Well, Human influenza has never affected me greatly in the past. I see no reason why this case should be different. Besides, those suits are uncomfortable; I simply promised Keller I would be careful not to touch you. Apparently, she is considering putting in a request to have your isolation lifted since the nanites appear to remain under the control of Dr McKay's programming.'

'Really? No one's told me that yet, but it's good to hear,' Elizabeth said, her mood noticeably brightening.

Teyla felt a prickle of guilt, wondering if she'd said too much letting Elizabeth in on that news. But she couldn't imagine that revelation posed any kind of security risk. 'I think everyone would be happy to see you out and about on the station again.'

'Perhaps...at least once this virus has cleared up,' Elizabeth laughed. 'Still, I'm going to be pretty limited in what I can do around here. To be honest, I'm worried the IOA will decide I should return to Earth.'

Teyla wished she could tell her Rodney was working on a way to heal her and shut down the nanites, but this time thought it might be too much information to share. If he couldn't find a way to make the nanites do what was required, she would have raised her friend's hopes unnecessarily. 'There is still much you can do to help aboard Atlantis. I'm certain they can find a useful role for you here. You have so much knowledge it would be a waste to send you back.'

'I hope you're right,' Elizabeth sighed. 'But the IOA have been known to make strange decisions before, and I'm not exactly their favourite person. They've probably had someone else lined up for my job for a while and will be glad for an excuse to be rid of me.'

'I believe there are members of the IOA who have great respect for you. They would be foolish to disregard what you still have to offer this expedition.'

'Hmmm...perhaps,' she mused. Then, she changed the subject. 'So, what have you been up to since I last saw you?'

'The usual. While we have no missions, I am keeping myself busy with Bantos training for anyone who is interested. I have also had requests for meditation lessons from several –'

Teyla noticed Elizabeth appeared to have drifted, her face slack and completely devoid of expression. It seemed she hadn't heard a word she'd said.

'Elizabeth, are you sure you are all right?'

After a few seconds, Elizabeth blinked and began to focus again. 'What...er, sorry. I lost my concentration there for a while.'

'So it would seem,' Teyla nodded. 'Would you like me to get Dr Keller for you?'

Elizabeth shook her head. 'No, I'm fine. Have you seen John today? He's been looking so tired lately...I'm really worried about him.'

Trying to hide the pain those words caused her, Teyla once again gave a strained smile, but she could feel it faltering even as she replied. 'I saw him earlier, but that was several hours ago now. I think he is feeling concerned about your situation, as we all are. Understandably, that and the additional responsibilities of sole leadership are leaving him somewhat tense.'

The room was silent for a while, as Elizabeth regarded her with her large, intelligent eyes. Teyla knew she had said too much. It was rare she ever said anything to suggest John was not operating at full capacity; he was the leader of her team, and she gave him her complete loyalty. But she was upset and wanted to talk to someone who might understand. As a woman who had argued with Sheppard a few times herself, she felt sure Elizabeth would appreciate her frustration.

'Is something wrong, Teyla?' Elizabeth's questioned confirmed what Teyla had thought; she'd given enough clues to let her know things were not running smoothly between them. 'Well...it is nothing serious. We just had a disagreement earlier and I decided it might be better to keep my distance for today.'

'Better for whom? You seem pretty upset,' Elizabeth asked, her brow puckering with concern.

Teyla fought back the tears threatening to spill, determined not to let her friend see just how upset their disagreement had left her. 'I am fine...really. As everyone else, I am simply stressed and exhausted after the events of the past few days.'

'What did you argue about?'

Teyla rolled her eyes to the ceiling and sighed. 'It was foolishness on both our parts, really. At breakfast this morning, Kate asked the colonel to sit with her and it seems she tried to offer him professional support.'

'That won't have gone down too well,' Elizabeth breathed, arching an eyebrow. 'But how did that cause an argument between the two of you?'

'He thought I had asked Kate to speak with him because I value her so much myself.'

'Oh, I see. So he assumed you were to blame and took you to task?'

Teyla nodded, wringing her hands between her knees. 'Yes. And then I also over-reacted...I'm afraid we both said things that hurt each of us.'

'Well, I wish I could say I didn't know what that felt like, but I've been there a few times myself. I'm sure he's sorry for jumping to the wrong conclusion, Teyla. John trusts you implicitly – I know that from discussions we've had in the past. But sometimes it's easier to take our frustrations out on the people we're most comfortable with because we know they're the most likely to forgive us.'

'I'm not sure I understand...' Teyla murmured, a frown creasing her brow.

'Well, we humans are an odd bunch. We tend to feel safer hurting the people we feel closest to when we're struggling ourselves because in our hearts we know they'll forgive us. The fact John chose you to vent at could well mean he trusts you to understand him the most.'

Elizabeth's explanation lightened Teyla's heavy heart. Her point seemed to be made genuinely enough, and now she had explained it, it seemed to fit the colonel's complex emotional state. Perhaps he did have strong feelings for her, but as for whether the fact he had chosen to vent at her made her the person he cared about most was still something she doubted. It was only after giving it some consideration she realised Elizabeth was now crying.

'Elizabeth! What is it?' she gasped, sitting forward on her seat and fighting the urge to rush to give her comfort.

'I don't even know why I'm crying. It's so hard being like this; one moment I'm fine, the next I'm a hopeless wreck,' she sniffed, struggling to regain her composure. 'I used to being the one people came to with their problems. Even John talked things through with me...not personal issues, of course, but other things that were on his mind. I've lost count of the number of times he and I stood out on the balcony overlooking the ocean and discussed our day. No one trusts me anymore...and with good cause. I can't believe this is my life now...staring at four grey walls...depending on the kindness of people already too stretched for time for company. I wish Rodney had never activated these damned nanites. Oh...oh...I'm out of Kleenex!'

Teyla located a handkerchief in one of her pockets and laid it on the nightstand. 'Here, use this.'

Thanking her, Elizabeth dried her tears as best she could. 'I'm sorry, Teyla. I shouldn't be off-loading like this when you have enough problems of your own. I'm being incredibly selfish.'

'Not at all,' Teyla soothed, wishing she could reach out and take hold of her hand. Part of her was angry that she didn't just do it knowing the restriction was likely to be lifted soon, but another part of her recognised that Elizabeth herself would probably prevent her from doing so. 'It is I who have been selfish coming to you with this issue when you have so much more to worry about.'

Elizabeth shook her head vehemently. 'No. Don't think like that. Your coming here actually makes me feel more normal. I haven't felt that way for days now.'

Feeling terrible that she could ever have wished Elizabeth out of their lives, Teyla tried to find something to say that would ease her pain. 'Rodney meant only the best for you. He intended to have the nanites repair you and shut down, but when you suddenly deteriorated he had to change their programming. None of us would have wished this situation on you. You must hold on to the hope that at some time, someone will be able to find a way to rid you of them.'

Nodding, Elizabeth sniffed back tears, her eyes puffy and her face still pale. She pinched the bridge of her nose as if her head was still troubling her. 'You're right, Teyla. There are plenty of smart people who can probably figure a way to solve this for me eventually. Right now, I should just be grateful I have that opportunity, and if I didn't feel so lousy, I'm sure I would be more comfortable about all this.'

'Much as you crave company, it seems to me that the thing you need most now is rest,' Teyla said calmly, giving her a sympathetic smile. 'You should sleep now and I promise to stop by again later to check up on you.'

Pushing her hair back from her face and wiping the last few tears from beneath her eyes, Elizabeth smiled sadly back at her. 'I think you may be right, Teyla. I am exhausted.'

Teyla stood and pushed her chair back to the side of the room, then collected up the empty water jug from beside Elizabeth's bed. 'I will ask someone to refill this for you,' she said.

'Oh, here,' Elizabeth replied, laying the handkerchief down for her to pick up. 'You should take this back. It's far too pretty to waste on my self-pity. Just ask whoever brings the water to bring me a box of Kleenex, too, would you?'

'Of course. Rest now; I'll make sure you get everything you need.'

As she left the room and walked down the corridor she felt the dampness of Elizabeth's tears in the embroidered cloth Charan had given to her when she had visited her shortly before her death. She had shed many tears upon it herself when she'd lost the old woman, but it felt right that she had shared something so important to her with her friend. She might not be able to embrace her, but she hoped the gesture had made Elizabeth realise that she cared.

And as she headed back to the infirmary, the nanites that had broken loose and left their host via Elizabeth's tears burrowed through her skin, so tiny she could not feel a thing as they invaded her body and began to use her system's natural resources to replicate and spread throughout her...


	18. Chapter 18

When Sheppard got a call that night from Dr Keller, his sense of foreboding received a frightening boost.

'_Colonel Sheppard, I need to see you in the infirmary right away. There's been a development with Elizabeth's nanites.'_

Having not yet settled into bed, he leapt up and sprinted down the quiet corridors, almost flooring Zelenka as he passed him on his way out of the transporter heading to his own room, and arrived in the infirmary in record time.

Dr Keller blinked in disbelief as she saw him panting before her, obviously shocked that he had covered the distance from his quarters to her office in so little time. 'Colonel! I know I asked you to come right away, but I didn't mean for you to give yourself a coronary!'

'The nanites...what's...going on?' he panted, leaning on her workstation and battling to regain his breath.

Clearly realising he didn't intend to indulge in small talk, Keller caught him by the elbow and guided him toward a laptop. On the screen he saw what he presumed was the latest scan of Elizabeth's body. He could clearly see the nanites had replicated and moved to several different areas of her body.

'Oh, God. They're spreading.'

'I don't want you to panic at this point, Colonel,' Keller said firmly, asserting herself before he could start planning their next move. 'The nanites _have_ replicated, but are now holding static again. If you look at where they are located – the thymus, spleen, lymph system, and in her bone marrow – it seems clear they are attaching themselves to the main components of her immune system.'

'Is this because of the virus she's fighting?'

'Quite possibly, but I'm worried something else could be going on.'

Sheppard's heart plummeted and he wondered at which point Keller would tell him something that justified her instruction for him not to panic. 'What?'

'I suspect the nanites are fighting something more serious than a cold. I think her body is trying to reject them. As I said before, they're a foreign object within her, and I'm thinking Rodney didn't have time to work out a way to fool her immune system into thinking they were compatible with her DNA. I think her body is fighting them, and the nanites are spreading out to suppress her immune system. I recommend putting her on a Rapamune protocol to stop the reaction –'

'No,' Sheppard stated firmly, cutting Keller off in mid explanation.

'No?' she repeated, he face reflecting the obvious confusion his order caused. 'But if I don't she could reject the nanites and she'll die.'

'When the nanites first invaded her body, Dr Beckett said they were attacking her immune system in an attempt to take over. How do we know they're not doing the same thing right now?'

'Because they've been reprogrammed. It's not within their capabilities to start attacking her that way.'

'I don't care. _Do not_ administer anything that suppresses her immune system. If those nanites are working correctly, nothing her body can throw at them should do any harm.'

'But I don't know if I'm happy taking the risk...'

'Fine. If you won't take my advice, let me get someone here who can explain things a little better.' He tapped his earpiece. 'McKay. This is Sheppard.'

Nothing.

'McKay, respond.'

'_Yes...yes...all right. There's no need to yell.'_

Sheppard rolled his eyes and counted to ten in his head in his head. 'Rodney, I need you to come down the infirmary and look at something Dr Keller found.'

'_What? Are you kidding? I just got to sleep for crying out loud!'_

'McKay,' the colonel growled in warning.

'_All right...all right. Just gimme a few minutes.'_

Sheppard took a deep breath to calm himself, then asked Keller, 'Have you mentioned what you've found to Elizabeth?'

'No. Not yet ,' the young doctor admitted, chewing nervously at the inside of her mouth. 'I didn't know how much you would want me to say to her.'

'I'll do it,' he grumbled, glad to have the excuse not to look at the woman a moment longer. Much as he'd tried to fight his desire to blame her for the nanites, he was finding it very hard not to, and her continual insistence the nanites were a beneficial presence only served to make him progressively more prone to disliking her. Why could no one else fully understand the danger they were in?

One of the guards outside the isolation room opened the door when he reached it, but he was too focused on the news he had to deliver to even acknowledge them. Inside, Elizabeth was fast asleep in her bed, lying on her side and breathing gently – peaceful, at least for the moment. How could he disturb her with something like this? Perhaps it could wait until morning.

He was about to leave when she stirred, her eyes cracking open just a fraction, and then widening immediately when they fell on him. 'John!' She sat up, almost smiling, but the attempt fell flat when she took in his expression. 'What's happening?'

'I've just spoken with Dr Keller. Your nanites are...behaving outside of their programming.'

Her jaw dropped a fraction, her face blanching. 'What...what does that mean?' she asked, smoothing down her hair as if the very act of making herself more presentable asserted some kind of control over the situation.

'They're invading your immune system. Keller thinks it may be because your body is trying to reject them, but she can't be sure.'

She nodded, maintaining a dignified composure as she looked at him. 'What does she want to do?'

'She wants to suppress your immune system in case the nanites begin to...come loose.'

'And what do you want to do?'

He battled the urge to yell, I _want her to stop interfering with you_, and said calmly, 'I want her to let your body do whatever it needs to do.'

She nodded again, chewing pensively on her bottom lip. 'The first time the nanites took over, Carson told me –'

'I know...that's why I think we should let your immune system do its thing. Suppressing it will just give the nanites free range through your body.'

The room was painfully silent except for the buzz of the electronic equipment accompanying them. Sheppard tried to think of something else to say, something that would make this all seem somehow less ominous, but nothing came to mind. He was scared for her, and for Atlantis, and he was pretty sure she knew that.

'Do I have a say in what happens to me?' she asked, taking him by surprise, although the more he thought about it, the more logical the question was. This was her life, and if she was suffering from any other condition, they _would_ be asking her what she wanted them to do. But since she had nanites in her brain...

'I doubt the IOA would agree to you making a decision on this,' he said flatly, trying not to show the emotions the thought evoked in him. 'The nanites may mean your judgement is...impaired.'

She took a deep breath in through her nose, then blew it out before saying, 'I see.'

'I know that must sound harsh, Elizabeth, but you have to see it from their point of view. Those nanites in your brain mean you're compromised...they could take over and we might not even know.'

'Who's to say they haven't already?' she asked, her eyes looking moist in the dim light. 'If they're already acting outside of their programming, how can you be sure this is really me you're talking to? You could be endangering yourself even being here.'

He shrugged, feeling awkward that she would fire a question like that at him. It was a case of shooting the messenger, but his shoulders were broad; he could take her anger on board. She sure as hell deserved the chance to vent at someone.

'I wish you could just bring in an EM generator and end all this,' she said more quietly, bowing her head. 'This isn't living – it's barely even existing.'

'That's not an acceptable option, Elizabeth. I wish we could get this sorted out quicker, too, but it's complicated.'

'You think I don't know that?' she snapped. Then, she stroked her fingers across her forehead, took a moment to gather herself, and offered him an apology. 'I'm sorry, John. It's not fair to take this out on you. You didn't want any of this to happen.'

'No one wanted _this_ to happen,' he corrected.

'No. I know. It's just that I was hoping to get out of here soon. Teyla said Dr Keller was considering removing my isolation status because the nanites were showing no unusual activity. I guess this has blown any chance of that now.'

Though annoyed Teyla had told Elizabeth that before knowing it was definite, Sheppard supposed he understood the Athosian's keenness to give their friend some good news. What annoyed him even more was the fact Keller had discussed the prospect with Teyla before mentioning it to him. He wondered if he was being over sensitive because of the insecurity his new position awoke in him, or perhaps, worse still, he was becoming a control freak. But he felt certain decisions like that should be run past him before being discussed with less senior members of the team, and Elizabeth herself would have expected nothing less when she was Atlantis' leader.

Pushing his feelings aside, he replied, 'Maybe it's postponed for a while, but we'll get there.'

Now she smirked, shaking her head. 'You're a terrible liar, John Sheppard.'

'I'm not lying. If McKay can figure out exactly what those things inside you are doing, and it turns out to be non-threatening, you might be allowed out and about yet.'

She sighed, settling back against her pillows with a kind of sad resignation. 'No offence, but I won't hold my breath on that.'

'We're doing everything we can to sort this out,' he assured her, his words sounding hollow even to him. The Replicator technology was changing even as they thought they were getting to grips with it; in truth, he doubted they were going to get a handle on it anytime soon. But he could be wrong about that. Hopefully, by the time he got back to the infirmary McKay would be there and they could figure this out without having to make the kind of assumptions Keller had been jumping to.

'I know you are,' Elizabeth replied quietly, pulling her sheets up over her chest. 'I think I'd like to sleep again now.'

'Sure...you get some rest and we'll talk some more in the morning.'

He headed for the door, but the sound of Elizabeth calling his named stopped him just before he opened it. 'Next time you come in here, you'd better be wearing a hazmat suit.'

Though he didn't want to do it, he realised she was probably right. He nodded and headed back to the infirmary.

Before he reached Keller, he could hear Rodney's frantic tones scraping down the corridor. 'No, no, no, no, no. I don't care what her immune system is doing, the nanites shouldn't be reacting in this way. Why didn't you tell me about this sooner?'

'Because I've only just found it myself. I told Colonel Sheppard and then he called you. We couldn't have moved any quicker on this.'

The colonel strode in, seeing McKay's puce complexion and bulging eyes. 'This is bad, Sheppard. They're adapting. They shouldn't be able to do that.'

'Well, since saving her life is what they're created to do it's not exactly a surprise, Rodney. What I need to know is are they suppressing Elizabeth's immune system to save the repairs they've done, or to strengthen their hold?'

Rodney flicked his eyes down to the laptop and keyed in a few commands before throwing his hands up in despair. 'There's no way of knowing which cause is driving them at this point.'

'D'you think you can bring them back under control?'

'Well, if I continue to write the program you've asked me to create, that would do it anyway.'

'Would it? Can you be certain of that?' Sheppard demanded, fixing him with a hare stare. 'Or is it possible these things are now beyond your control and we need to act to neutralise them?'

'Neutralise them? You mean, shut them down?' Keller asked, her eyes threatening to pop with shock. 'But that'll kill her.'

'And if the Replicator nanites inside her are acting on Oberoth's programming now, they won't hesitate to do the same to us,' he pointed out.

'You think he reprogrammed them, don't you?' Rodney breathed, his eyes darting about as he thought about everything that had happened since her return. 'You suspected this all along.'

'She's in isolation, and everyone has been warned not to touch her. Whatever I thought, I've made sure those nanites don't jump ship, so we shouldn't need to panic, right?'

'Well, I've been monitoring them on a regular basis, so this change has only just happened in the last half hour,' Keller assured him. 'And Elizabeth herself is exhibiting no unusual behaviour or severe adverse reactions. Don't you think shutting them down might be a little premature?'

'Actually, right now, I'm hoping it isn't too little too late. You're absolutely sure no one in your team has come in contact with her?'

Keller shook her head. 'We've all been wearing hazmat suits, so there's definitely been no direct contact. I made sure very member of my team understood the potential danger. No one else has touched her.'

Sheppard nodded. 'Okay. So chances are no one else could have been contaminated even if it's possible,' he said, almost to himself. 'And like you said, there has to be a conscious decision to pass on the nanites, and there's no way Elizabeth would do that.'

'That would seem to be the case,' she agreed.

'Plus the nanites aren't replicating exponentially,' Rodney added. 'They've only created enough new units to go to work on her immune system while the others hold her injuries together.'

'So...non-threatening at this point?' Sheppard clarified.

'I'd say so, yes,' McKay nodded, but he couldn't look him straight in the eye.

Sheppard chewed his lip, giving it some thought. He didn't want to pull the plug on Elizabeth unless he had to; those nanites were her life-support system after all. But he'd given Shen his promise that he wouldn't hesitate if she posed a threat to Atlantis. He had to make a judgement call. 'All right. I'll report the change to the IOA, but recommend that, since there appears to be not threat to anyone other than Elizabeth herself at this point, we continue with the process of monitoring her for the time being,' he announced. 'Rodney, walk with me.'

They left a stunned Dr Keller behind them. Clearly, she'd thought she was going to have to fight harder to save her patient. Once again, Sheppard found himself wondering if he would have made the same decision had it not been Elizabeth in that isolation room. He figured both he and Rodney were allowing their guilt to colour their decisions more than they should, and he promised himself this was absolutely the last time he would do that.

'You think we're going to lose her, don't you?' Rodney asked quietly once they were away from the infirmary.

'I hope not,' Sheppard breathed. 'But if we don't get on top of it soon, I'm afraid those things are gonna run riot again.'

'I should get down to the lab and work on them. Damn it! I should have got a new sample before I left the infirmary!'

He started to turn, but Sheppard caught hold of him and turned him back round. 'You need to get some sleep, McKay. You can't keep functioning on caffeine alone.'

'But time could be of the essence...'

'And you'll probably work faster with at least a few hours sleep under your belt.'

His shoulders dropping, Rodney admitted defeat. 'Yeah, I guess you're right.'

'Considering what's happened, I'm going to recommend we suspend all off world travel.'

Rodney's eyes widened. 'D'you really think that's necessary?'

Sheppard shrugged. 'I don't know, Rodney. But until we get a handle on exactly what's happening with those nanites, I don't think we should be sending anyone else through the gate.'

'Yes...yes...you're right. It would be irresponsible of us to travel to other planets until we have this fully under control. Which is why I should probably get to the lab...' He tried to turn again, but Sheppard caught his arm and dragged him along with him.

'No, that's why you should rest and come at the problem with a clear head. C'mon, I'll walk you to your room...just to make sure you don't change your mind en-route,' Sheppard suggested as they set off again.

The corridors were quiet, with only one or two personnel still active as the end of their shift approached.

Once they were alone, Sheppard asked. 'How's finding a new frequency for the Replicator disrupter coming along?'

Rodney shrugged. 'It's still in the hands of the program. It could take hours; it could take weeks or months.'

'Then I guess we'd better hope it's sooner rather than later,' Sheppard said, trying not to think of the implications of the latter timescale. 'What about the jumper? You got that up and running on remote orders from the chair.'

'The jumper's ready, and the repairs to the chair are almost complete, so it'll be back on-line tomorrow.'

'Well, that's something,' Sheppard said, feeling a sense of relief that they would at least have some defence against external attack. 'And the shields?'

'Hopefully extending across the whole city some time tomorrow, too.'

'That's good, Rodney. We'll be able to cloak, send out a decoy jumper, and defend ourselves if necessary. You should be proud of the work you and your team have done.'

Rodney stopped and eyed him dubiously, shaking his head. 'They really have to get someone else in charge here soon because this supportiveness is really beginning to weird me out.'

'You and me both,' Sheppard admitted, sputtering out a laugh. 'I'm not sure how much longer I can keep this up.'

They reached Rodney's room and the scientist activated the door. 'Well, at the risk of sounding like a cliché – call me...if anything happens, that is.'

Sheppard nodded, awkwardly clapping his hand on his friend's shoulder. 'Don't worry, Rodney. If anything changes, you'll be the first person I call.'

McKay gave him an anxious smile, then headed into his room. Sheppard decided that once he'd fed back to the IOA, and acted on whatever instructions they gave him, he would turn in himself...again. He wondered how much sleep he would actually get tonight, and what his nightmares would tell him this time.


	19. Chapter 19

Rodney had managed the grand total of three hours sleep before guilt drove him from his comfortable bed and back into the lab to begin working again. The new sample of nanites taken from Elizabeth only twenty minutes before his arrival in the infirmary that morning was doing nothing extraordinary; there seemed to be no hint of aggression in their behaviour, it just wasn't exactly what he'd programmed them to do.

Having watched them, poked them with various implements, simulated their current behaviour and run possible scenarios through the system, he still couldn't figure any reason for their change in behaviour.

He sat back from his workstation, rubbing his eyes to try and clear away the bleariness. He needed to get some proper sleep, but until this business with the nanites was unravelled to his satisfaction, he doubted he was going to get it.

04:33 am his laptop clock told him. Maybe he would just get his head down on the desk for a while; a power nap would soon have him firing on all cylinders again...

The smell of coffee permeated his nostrils as the scientist blinked himself back into consciousness. A mug stood steaming in front of him. _Where did that come from? _he wondered, lifting his head up from the counter so he could fully appreciate the aroma. _Ahhhh, bliss!_

'I thought I might find you here, so I brought you a coffee,' he heard his Czechoslovakian colleague call from somewhere behind him.

Rodney checked his watch. 05:37am. Had he really slept for an hour? His head throbbed, protesting that he was forcing it to work again so soon. It really didn't want to tell him whether his calculation of the passage of time was correct, or whether or not four hours sleep was feasibly enough to function on. It just kept trying to drag him back to the sleep he so badly needed.

In rebellion, Rodney snatched up the mug and took a swig of coffee. It was bitter tasting and strong, and burned his tongue as it hit it – just the way he liked it. 'Thanks for this, Radek,' he said, lifting his cup in salute.

'You're welcome. What're you working on?'

Rodney sighed, leaning back in his seat and raking his fingers back through his hair. When he'd come to Atlantis it had been much thicker than it was now, and he briefly wondered how much of its loss could be attributed to Mother Nature, and how much was purely down to stress. 'Elizabeth's nanites are functioning outside of their programming and I'm trying to figure out why.'

'What!' Radek was out of his seat and standing beside him before Rodney could even blink. 'Why didn't you wake me?'

'Because Sheppard told me to get some sleep, and I only started working on this a couple of hours ago myself. It seemed pointless to deprive you of sleep, too.'

Radek gave him a grim smile. 'For something this important I am willing to forego and hour or two,' he told McKay. 'I think you should bring me up to speed.'

'There's not that much to tell. They've replicated, but not in any quantities we need to worry about, and they've moved into Elizabeth's immune system. Keller thinks they might be trying to stop some kind of attempt by her body to reject the nanites, and she could be right...but she might not be. I just have the feeling this is the start of something bigger, and so does Sheppard.'

'Have you studied the coding to see if anything's been altered? Radek asked.

Rodney rolled his eyes in the Czech's direction. 'Yes...of course I have, Radek. I'm tired not retarded!'

Radek held up his hands in mock surrender. 'Sorry I asked.'

Sighing, Rodney ground out a reluctant apology. 'No, I'm sorry. You're right to go back to basics when you can't find the answer.'

'You want me to check the coding for you? A fresh pair of eyes might help and I figure I've had more sleep than you, so I can concentrate better than you can right now.'

'Oh, you're just loving this, aren't you?' Rodney grumbled, sipping at his drink. 'You've been desperately trying to prove you're better than me for the past three years and now here's your chance.'

'This isn't about anyone being 'better' at anything, Rodney. It's about saving Elizabeth. I'm just more rested than you are. No one can be expected to solve something as complicated as Replicator coding on the pathetic amount of sleep you've had in the past week. Admit it; you're worried about her.'

Although he didn't much care for Radek's use of the word pathetic, Rodney supposed it did suit the situation. 'Okay, fine, I'm worried. You start checking through it again, and I'll just sit here looking redundant, shall I?'

'Actually, I think I finalised the repairs to the control chair last night. You could look over those and make sure they encompass everything you need for that remote jumper before I implement them if you like.'

Rodney knew Radek was just trying to make him feel better, and somewhere deep down in his cynical heart he appreciated the gesture. Unfortunately, that sentiment wasn't what came out of his mouth.

'Yeah, sure,' he huffed, taking the data file Radek was holding out toward him. 'I'll just check the simple stuff, shall I? That way I can't do any more damage!'

Radek gave him a bemused smile and headed off to his own workstation to check the nanite coding while Rodney continued to grumble.

oooOOOooo

_Sheppard walked the corridors of Atlantis, heading to the infirmary. He'd managed a few hours of sleep and now wanted an update from the infirmary staff. When he got there, Marie was on duty while Keller got some much needed down time._

'_Morning. Any news on Elizabeth's condition?'_

_Marie shook her head. 'Nothing much. The new nanites are still attached to her immune system, while the old ones continue to keep the repairs in place. We've been watching her all night. She's been a little restless, but otherwise there's nothing to report.'_

'_Is she awake?'_

'_I'm not sure. But we can go and check.'_

_She guided him through to the side lab where the screen had been set up for playback of the footage in her room. Elizabeth was just yawning and stretching her arms, clearly in the early stages of waking. _

'_I should go see her – find out how she's doing this morning.'_

_Marie nodded and gave him a sympathetic smile as if she knew how difficult it all was for him. 'You know where the hazmat suits are.'_

_After kitting himself up, Sheppard trudged his way to the isolation room with heavy limbs and an even heavier heart. He didn't have the first idea what to say this morning. Last night had required him to be clear and efficient in his explanations, but now, this was time for him to be a friend, and lately that wasn't as easy as it used to be. He wished he could forget what she'd said in the interview, forget the questions it had forced him to ask himself about how he felt for her. When he'd first met her she'd been off limits. Then, they'd taken up dual leadership roles, and anything more than camaraderie was out of the question. But circumstances had changed; and he was afraid of the emotions now awakening in him for someone he felt was slipping out of his reach. He forced himself not to analyse what he was feeling; he couldn't afford to falter now._

_When the guards let him in she was already sitting up. She smiled as he approached, causing him as much pain as if she'd landed a sucker punch. 'Morning, John. I might have known you'd be the first person to appear this morning. I see you opted for orange even though it isn't your colour.'_

_He fought to smile in return. 'How'd you sleep?'_

'_Well, I did have one or two things on my mind –'_

'_I can imagine!'_

'— _but I did okay, I guess. I imagine I got more sleep than you did judging by those dark circles under your eyes.'_

'_Well, you sure know how to make a guy feel good about himself,' he quipped, already beginning to tire of the suit. It felt heavy and cumbersome and he wondered how long would be considered a polite length of time to stay there with her since he couldn't wait to get the damned thing off again. _

'_Have there been any further developments in my condition?' she asked._

_He shook his head, grateful that she seemed only too happy to deal in facts rather than wallowing in self-pity. 'Nothing as yet. They're still invading your immune system, but the numbers haven't increased to a point where we need to worry, and they seem to be holding steady. I imagine Rodney is already at his desk working on a solution, so, who knows, later today this may have all blown over.'_

'_I think that's being a little optimistic, even for you.'_

_He shrugged. 'Rodney has a knack for pulling miracles out of his a – hat, so don't give up on him just yet.'_

_He could see her struggling with the urge to laugh. Obviously he hadn't covered his gaff quite as well as he'd hoped. But, when she did speak, her response wasn't as positive as he'd hoped for. 'You know this is all going wrong, don't you?' she said sadly, her huge eyes meeting his and filled with so much pain he felt his heart would break for her. 'Eventually, one way or another, I will cease to be.'_

_He shook his head, unwilling to accept what he knew was most likely inevitable. 'He'll figure something out.' He approached her, standing before her and resting his hands either side of her legs on the bed. 'You just keep fighting to remember who you are, and let us worry about the rest.'_

_As he looking into her eyes a strange glaze passed over them, and then was gone again just as quickly. He pulled back, hoping it was a trick of the light or a figment of his overtired brain, but something had changed. She was smiling now, but not the sad smile she'd forced on for the past few days; this was a malevolent sneer, much like the one Teyla had worn when taken over by the Wraith. _

'_You can continue to hope, but whatever you try will be in vain,' Oberoth's voice said from Elizabeth's lips. 'You cannot hope to stop us. Your intellect is ludicrously small in comparison to ours. We will be victorious.' _

_Though shocked, Sheppard reacted strongly, the sudden emergence of the Asuran leader's voice not coming as a complete surprise to him. This was only confirmation of what he had suspected all along. The Asurans had altered her and taken control. 'Let her go, you bastard!' he growled. 'Let her go, and I promise I won't hunt you down and destroy you.'_

'_You are mistaken, Colonel Sheppard,' the voice said confidently. 'You cannot come after us. Already, nanites are spreading throughout your city, taking over everyone and everything in Atlantis.'_

_Anger spurring him into an irrational reaction, Sheppard launched for her, grabbing her throat and squeezing. All he could think of was freeing her from Oberoth's grasp, even if that meant killing her. Unfortunately, he hadn't factored in the newfound strength the nanites afforded to her. She jammed her hands into his chest, knocking him backwards and sending him sliding across the floor until he collided with the door._

_He expected it to open, and to feel the strong hands of two marines pull him to safety, but it didn't happen. Elizabeth jumped off the bed, padding barefoot across the cold floor toward him. 'Everything and everyone in Atlantis will fall,' she said in her own voice now, her fierce gaze burning into him. 'And you, Lantean, will be spared until you have witnessed it all.'_

'_I...I'm not a Lantean,' he stammered, his brain still spinning from the impact. 'You know that.'_

_She bent down to him, grabbing handfuls of his protective suit to pull him closer to her. Her eyes glared at him just as Oberoth's had when they'd made their escape from Asuras, leaving Elizabeth behind. 'You are a direct descendant of the Lanteans. Only someone bred from pure Lantean lineage could have such a strong genetic link to them. In the absence of your predecessors, you will bear witness to the final destruction of the cornerstone of their empire.'_

_That said, she pushed him away, thudding his head against the door again and sending him tumbling into unconsciousness... _

Sheppard woke to the sensation of sweat-dampened sheets and clothes, but recovered more quickly than he had on previous days. The nightmares were becoming so much a part of his nighttime routine he would have felt deprived without them. He climbed out from beneath his sheets, stripped both himself and his bed down, and headed into the bathroom to get cleaned up and start his day.

After popping into the infirmary to check on Elizabeth's status, he headed to his office and read a couple of those pending reports. He felt guilty for not going to see Elizabeth in person, but the dream was still fresh in his mind, and needed to change the pattern of events out of some weird and newly discovered superstitious facet of his personality. Though vowing to see her later eased his conscience a little, he couldn't fully override the feeling he was letting her down. But what could he say? Nothing that the medical team couldn't tell her anyway.

He took breakfast alone – deliberately so. He waited until the time his teammates usually ate had passed and then added an hour, just to be absolutely sure they were gone. No one came to look for him, which he took as a sign that they recognised his desire to be left alone. His feelings about Elizabeth and the nanites were dragging him down. He wouldn't be good company, and the last thing he wanted was to try to be upbeat for everyone else when he felt so low. Added to that, he still wasn't sure how to deal with Teyla yet...

He found a table in a quiet corner and drank some orange juice while he waited for his infamous appetite to kick in. Today, he didn't feel hungry at all, but knowing he would need the calories to keep him going for the next fourteen hours at least, he forced down some toast while trying to ignore the mild nausea the intermingling aromas of eggs, waffles, pancakes, bacon, and various other breakfast foods evoked in him. Once he'd picked at half of his meal, he surrendered and made his way up to the control room for an update.

Chuck talked him through all the latest long-range scans they'd run, none of them showing anything untoward. Sheppard nodded as he listened, knowing from the tone of voice the technician used that the information he was giving him was nothing to be alarmed about. Though he tried to concentrate, his mind constantly drifted to the memory of seeing a city ship approaching Atlantis in one of his earlier dreams. He had to fight the urge to rush out onto the balcony and check the skies again.

Duties successfully performed there, he headed on to the labs to catch up with Rodney. He found both him and Radek scouring the nanite coding. They were bickering as they always did, but it was mostly good-natured and not particularly hurtful, so, figuring it was best to leave them to their work, he warned them to play nice and went on hi

Today he was restless. Nothing in Atlantis felt right. For some reason, even the background hum that always accompanied him sounded discordant, as if the city was trying to tell him something was wrong. The alarms might not be sounding, but he instinctively knew it was true.

Plucking up courage, he decided now was as good a time as any to visit Elizabeth, and so headed for the nearest transporter to take him to that level. As he tried to think of what he wanted to say to her, he heard footsteps hurrying to catch up to him.

'Colonel. We missed you at breakfast this morning.'

Teyla.

He turned to face her, wondering what kind of a reception he would receive. To his relief, she gave him a bright smile as she jogged to a halt in front of him. From her attire and the equipment she carried he could see she'd been training. 'You and Ronon been fighting already this morning?' he asked.

'Yes. We sparred before breakfast. I have been training with a number of the marines for the past couple of hours. What have you been doing?'

'I thought I should make a dent in the pile of work on my desk I've been putting off for the past several days,' he answered, and it was almost the truth.

'I see. And have you seen Elizabeth this morning?'

'Not yet, I was just on my way. I take it Rodney's updated you on the developments.'

She nodded. 'He has. If you do not mind, I would like to accompany you and visit with Elizabeth also.'

He shrugged casually, 'Sure,' but he was greatly relieved to know she would be there with him. Teyla could always sooth any situation with her calming presence. He felt sure Elizabeth would benefit from having her there while dealing with the issues her changing situation brought.

They reached the transporter and he activated the doors so they could step inside. 'You know about the need for hazmat suits now, right?' he asked, turning to face her just as she swung her Bantos rod at the side of his head and, after a blinding flash of light and pain, everything went black...


	20. Chapter 20

In the isolation room, a sharp pain scraped through the inside of Elizabeth's skull. She pressed the heels of her hands to both her temples, but it brought no relief. The sensation lasted only a minute, then was gone, but the experience left her unnerved.

In that moment of agony she had seen John entering a transporter, only to be smashed to the ground by what looked like a Bantos rod. For a moment, she'd felt as if she were seeing through someone else's eyes, as if she were actually in the transporter with him, wielding that weapon and striking him down.

Why would she imagine something so horrible? John had been nothing but kind to her; how could she even think of harming him?

Something felt strange inside her. Her brain tingled as if tiny electrical pulses were randomly firing through it. Random thoughts flashed through her mind, thoughts of violence against the Wraith, the Ancients, and the inhabitants of Atlantis. She imagined tearing the room apart, destroying the equipment monitoring her vitals, ripping out the cameras, ridding herself of these inferior beings and becoming something much more than they could ever hope to be.

Recognising these weren't her own thoughts, she tried to signal to the cameras that something was wrong, but found her body unwilling to comply. She sat still and calm, giving no outward sign of her inner turmoil. Memories returned to her now, recollections of her imprisonment hidden from her until this point. She saw images of Oberoth standing over her, his hand penetrating her forehead, and reams of data flooding her mind, instructions and coding rushing into her mind only to be locked away and forgotten. Until now. The Asurans _had _tampered with her nanites while they held her prisoner, she could remember it all now with startling clarity, the memories and information unlocking as if to taunt her.

She heard thoughts inside her head, Oberoth's thoughts, telling her the people of Atlantis would pay for their audacity and for the cruelty of their predecessors. Desperately trying to block him, she sensed the battle was already lost. She could feel his thoughts as clearly as if they were her own. Though she fought him mentally, she could feel his control over her body already asserting itself. He had crept in there unseen, and now there would be no stopping him. It was only a matter of time before he took full control of her mind and used her to destroy everything she loved.

He laughed, the sound gouging into her brain and mocking her attempts to defy him. His voice told her it was already too late, that they had infiltrated the city, so what little control she could assert would do no one any good.

Atlantis was doomed to fall.

oooOOOooo

'Has he woken up yet?'

'Not yet, Rodney. But he is showing signs that he's beginning to surface. He hit his head pretty hard, so he'll come round when he's good and ready.'

Sheppard heard the voices and slowly pieced the nonsensical sounds together into sentences he could understand. McKay and Keller? Where the hell was he?

One thing he did know for certain was he had a killer of a headache, and felt even more like vomiting now than he had earlier. He lifted his hand to touch a tender spot on the left side of his head, feeling the tug of a blood oxygen monitor on his index finger. Great, so he was in the infirmary. His favourite place to be.

He cracked his eyes a fraction, but the pain caused when light hit them forced them closed again. He decided to just lie there and get his bearings before announcing he was awake, but unfortunately his movements had been spotted.

'He is rousing,' he heard Teyla say.

The sound of her voice brought his memory rushing back to him. The transporter...Bantos rods. She'd hit him! What the hell was that all about?

He snapped his eyes open despite the discomfort the sudden intrusion of light caused, leaning away from her as he spotted her already at his bedside. 'Why'd you hit me?' he demanded, glaring at her.

Teyla's brow crumpled in confusion. 'What do you mean?'

'What do I mean? I mean, why d'you hit me?' he fired back at her, repeating his question.

All eyes turned to Teyla, awaiting her reaction.

She shook her head, looking puzzled. 'You are mistaken, John. I did not strike you; you either lost your balance or passed out in the transporter and struck your head as you fell.'

He stared at her, looking for signs of deception in her expression, but found none. Yet he knew what had happened. Was she really that angry with him after their argument? That wasn't like Teyla; she was the only person he knew who could remain calm no matter what the situation they faced. Perhaps he was wrong. Perhaps he was completely losing it.

'Is it possible he is delirious due to the lack of sleep he has suffered recently?' Teyla asked, he face depicting her usual level of concern.

'Possible? I'd say that's a certainty. I can barely remember my name most of the time,' Rodney blustered. 'Is it possible whatever cause this is...you know...catching?'

'No, Rodney. There's a serious pain in my ass, but it's not contagious...and I'm not delirious,' Sheppard growled, clutching his forehead as an ache pulsed through it. Speaking was painful, the noise of his own voice inside his head triggering wave after wave of nauseous throbbing that left him dizzy and mildly disorientated.

'Not now,' Ronon rumbled, 'But you only just woke up.'

'Not that we can really class that as a rest,' Keller pointed out. 'He was unconscious, not sleeping. It doesn't have quite the same restorative effect.'

'Whatever,' Ronon grunted, 'But now he's awake he should know better than to think Teyla could hit him. He trusts Elizabeth more than he does us these days.'

Hearing his friend make that accusation hurt, but Sheppard had to admit, that was pretty much true where Teyla was concerned right now.

'Well, concussions do leave the sufferer somewhat confused...but I'm sure Colonel Sheppard will realise his mistake once he's feeling better,' Dr Keller interjected. She turned to Sheppard and offered up a sympathetic smile. 'I'll get you something for that head. You have to stay lying down until that concussion's passed, so no running around trying to keep tabs on everything today, okay? Major Lorne has taken over, and he's happy to look after things until you feel ready to step back into the role.'

The way his head felt, Sheppard suspected that wouldn't be any time soon. He closed his eyes and rode another wave of sickness, the light touch of a hand on his arm disturbing him. He opened them again to find Teyla's tiny hand resting on his biceps. 'Are you all right, John?'

A flash of recall – the viciousness in her eyes as he'd heard the whistle of the Bantos rod approaching, too late to duck its blow – made him snatch his arm away from her. He didn't care who thought he was going crazy; he knew different. She'd hit him. But now, rather than anger, he felt a sadness welling in him. Had he really offended her so badly she felt justified in lashing out at him? Wait a minute...this was Teyla he was thinking about. Teyla did not react that way no matter how bad the disagreement...or did she? There had been that one time with Sergeant Bates. She'd punched him, and if he hadn't been there to stop her she might have done much more to the man. But the slur Bates had thrown at her was far worse than anything they'd fought about. He closed his eyes again. If his brain didn't ache so much he might have a hope of working it all out. He supposed he did have to consider the fact he might have been falling unconscious before he saw her swing for him, and his exhausted brain had somehow twisted the real details.

'Well, now you're awake and no longer scaring us witless, I should really get back to work,' Rodney announced, never one to linger long when others were feeling ill. 'I have some nanites to annihilate.'

For a second, Sheppard thought he saw a flash of anger in Teyla's eyes, reminding him of the same look he'd seen cross Elizabeth's face in his dream. It was gone before he could be sure, but he didn't like the fact the flicker of reaction had coincided with Rodney's mention of ridding them of the nanites.

'Yeah, actually, I think I'd like to be alone now anyway,' he croaked, sliding down in his bed. 'I figure I should make the most of this enforced rest time.'

'Well, enjoy your sleep...and don't worry about me slaving away down in the labs, struggling to keep my eyes open.'

Though he meant it as a joke, Sheppard suspected there was more than an ounce of truth in Rodney's words. 'I appreciate everything you're doing, Rodney,' he called after him as the scientist beat a retreat.

'Again with the creepiness!' he heard him call back, bringing a smile to his face.

'We'll go and let you settle down, buddy,' Ronon said gruffly, giving him a friendly punch to the shoulder. 'Stay here and get some rest until the doctor's say you're fit. Hopefully, you'll remember who your real friends are by then.'

Even for Ronon, that comment struck Sheppard as particularly harsh. The big man did have a tendency to speak his mind, but suggesting Elizabeth was no longer someone he should consider a friend was pretty callous. The Satedan began to walk away, but Teyla hesitated a moment or two longer at Sheppard's bedside, a weird smile twitching at the corners of her mouth. 'Take care, John,' she said, the pitch of her voice much lower than normal, and with an uncharacteristic hint of menace.

He swallowed and nodded, watching her go. Was he being paranoid or had those words been as threatening as they felt?

Five hours later, and with his head still pounding, Sheppard was practically climbing the infirmary walls. Waiting until Keller was occupied elsewhere, he took it upon himself to get dressed and discharge himself, despite the protests of the medical staff still present.

He swayed his way out of the infirmary on unsteady legs, barely able to feel the floor beneath his feet. He knew that wasn't good, but with no need to take charge of the city now Lorne had assumed control, he could stumble around to his heart's content without fear of doing any harm. He'd spent the time in the infirmary thinking things through, and he was certain now that he knew what had happened in the transporter, and he knew what he'd seen in the infirmary. He needed to get to the lab and make sure everything was going according to plan.

He wandered to the transporter and, after checking over his shoulder to make sure he wasn't about to be ambushed, he activated it and asked it to take him to the labs.

When he arrived at Rodney's workbench, dizzy and breathless from the effort, the scientist didn't even attempt to hide his surprise or his dismay. 'Sheppard! I can't believe they let you out of the infirmary already – you look worse than ever.'

'Thanks for that, Rodney,' the colonel quipped, leaning heavily on McKay's desk. 'And for your information they didn't let me out; I discharged myself.'

'Well, that was stupid.'

'I can't just sit in bed at a time like this, Rodney. The place is going to hell and I need to do something!'

McKay looked blankly back at him. 'What d'you mean, going to hell? The chair's fixed, the shields are fully operational, Zelenka has fitted the newly constructed components into the hyperdrive to bring it on-line, and...oh...oh, this is about that business with Teyla, right?'

Sheppard could see from the man's expression he was uncomfortable even broaching the subject, but he needed to warn him. 'Something's not right here, Rodney. I know what happened in that transporter. I know she hit me just as sure as I know I'm talking to you now.'

'But why would she do that? It doesn't make sense!'

'I know, I know. You're right. It doesn't make sense. All I know is she's acting weird and I want you to watch your step around her. You didn't see the look in her eyes when you said you were going to annihilate the nanites in Elizabeth. I've never seen her look so mean...except for in the transporter.'

McKay's jaw fell slack, his eyes darting as they did when he began to panic. The only thing Sheppard wasn't sure of was whether he was panicking at the thought of Teyla going 'dark-side' or the fact the colonel was telling him that was what he thought.

'So...so you're saying Teyla might come after me next?' he squeaked, his voice cracking.

'I don't know, McKay,' Sheppard sighed, rubbing his aching forehead. 'I'm not exactly thinking straight right now, but getting Atlantis fully functioning is pretty much in your hands. So, if they want to sabotage things, you're the one to take down.'

'They who?'

Sheppard realised then how little sense he was making. There was no evidence the Asurans had infiltrated the city in any way, yet that was what he felt. Then, a horrible thought occurred to him. He was pretty sure the Asurans could change their form – they had done so to take on the shape of their creators after all. What if they had somehow got into the city and taken on Teyla's identity? He hadn't even thought of that. What of Teyla was lying injured somewhere, in need of his help?

'I have to go find her,' he suddenly announced, pushing up from the desk and swaying with the change in position.

Rodney caught his arm, but let go the minute he felt it was safe to do so, looking embarrassed about the contact. 'Who? Teyla? Why would you want to go find her? You think she cracked you round the head earlier!'

'I just need to figure something out,' he muttered heading out into the corridor.

Walking as fast as he could, he had to catch himself against the wall several times to steady himself so he didn't crumple. His brain really wasn't ready for his body to stay vertical yet, so vertical while moving at a slow jog was even less acceptable. The walls seemed to undulate around him as if Atlantis were breathing...more like struggling for breath he realised as he saw the erratic shifts going on around him. The city was suffering...it was being attacked; he could feel its fight to survive as surely as if it was his own battle. Perhaps it was...or perhaps he was finally losing his mind after all.

He stopped to take a few breaths, struggling himself now to successfully inflate his lungs. Was the city pulling him down with it? No, that was ridiculous. A lot of his thoughts recently had bordered on insanity...the freaky nightmares, the city communicating with him, seeing dead doctors in his dreams...maybe he had imagined all this stuff with Teyla. He briefly considered heading back to the infirmary and turning himself in, even turned around to head in the right direction, but then decided against it. He had to find Teyla. He wouldn't settle until he knew she wasn't some kind of evil Replicator twin.

Forging ahead, he'd only managed a few more shaky paces when he heard a voice shout out from behind him.

'What're you doing out of the infirmary?'

Ronon. Thank God – someone who could help him. He turned around, reaching out to steady himself against the wall. 'You know me; I always was a lousy patient,' he quipped, throwing his friend a crooked smile.

'Keller says I have to bring you back. You're in no condition to be wandering around on your own,' Ronon told him, unsmiling.

'Look, I just want to go apologise to Teyla, then I promise to go back to the infirmary. Okay?'

Ronon pulled his energy gun from his thigh holster and aimed it at him.

'Easy, Chewie!' Sheppard gasped, raising his free hand in surrender. 'I just said I'd go back with you in a few minutes. Don't you think you're over-reacting?'

Ronon remained as inscrutable as ever, his eyes locked onto Sheppard's.

'Oh c'mon, buddy. Five minutes is all I need. You can gimme that, right? You can even come with me if you wanna be sure I don't go back on my word.'

A flash of pure hatred lit Ronon's eyes, the same one he'd seen crossed Teyla's dark orbs, and the one he'd first seen in his dream.

'Not you, too,' he breathed, backing up a few steps and wondering if there was any way he could outrun the Satedan.

The bolt of energy the gun fired in his direction answered that question before he could even try.


	21. Chapter 21

Sheppard's yelling hit Rodney's eardrums and set them ringing as soon as he got out of the transporter. He'd been on his way to the infirmary for something to perk him up when his friend's screams caught his attention. He immediately broke into an uncharacteristic run, arriving at the infirmary sweaty and short of breath. There, he found Ronon and a couple of the medical team pinning Sheppard to a bed while Keller secured him with wrist and ankle restraints, plus a strap across his torso that pinned his arms to his sides.

All the time Sheppard bucked and kicked and cursed at them, demanding to be released. It was a bizarre scene, one Rodney would never have expected to find, not even in his worst imaginings.

'What are you doing to him?' he hissed, motioning with his head for Keller to step aside with him. 'Is all this really necessary?'

Hearing his voice, Sheppard's wild eyes fixed on him out of everyone there. 'Rodney, you gotta get me outta here! They're trying to say I'm crazy. Don't listen to them; they're lying – they're lying!'

McKay backed up a couple of steps, driven back by the force of his words. 'Er...okaaayy!'

'We're not saying he's crazy,' Keller stated clearly, rushing back to the bed and struggling to tighten the final strap. 'He's suffering from a severe concussion that has left him delusional. We need to confine him to an infirmary bed until we're sure he isn't a threat to himself or anyone else.'

'A threat? This is Sheppard!' Rodney gasped. Sheppard was Atlantis' sentinel. He couldn't even consider the thought he might do someone any harm.

'He attacked me when I was heading for the mess hall,' he heard Ronon grumbled. 'It's not safe to let him out of here.'

'So post a couple of guards next to his bed until he's himself again!'

'I didn't do it, McKay,' Sheppard screamed, thrashing against his bonds. 'He shot me in the corridor on my way to see Teyla and dragged me here. You have to believe me! There's something wrong with them!'

'This is Sheppard we're talking about. You think two guards would stop him?' Ronon smirked to Rodney, ignoring the colonel's outburst.

Rodney supposed the big man had a point. This was the second time in just an hour he'd heard Sheppard accuse one of his friends of aggressive behaviour. And he had been rambling in the lab a short while ago, making very little sense. Perhaps this was the best thing for him. 'We can let him go once he's better though, right?' he asked.

'Once we've established he understands what's going on around him and accepts the truth, we'll take off the restraints,' Dr Keller assured him.

Rodney watched him struggling and cursing, flinching away again as the bed shook with the force of his thrashing. 'So, what's happened to him? Is it serious?'

'My guess would be some kind of breakdown, but we'll have to wait until Dr Heightmeyer's had time to assess him before we'll know for sure.'

McKay realised his heart was thundering against his ribs as he watched his friend straining at his bonds. Sheppard had always been a voice of reason and someone he leaned on for strength in times of trouble. Without him there to support him, Rodney felt...exposed.

'Could it be something else? A virus or something like that? I know how screwy I get when I pick up the slightest little bug – '

Keller shook her head, smiling grimly. 'I don't think so. He's displaying many of the classic symptoms of a break down; disturbed sleep, anxiety, changes in appetite, paranoia, seeing things that aren't there, violent behaviour...'

'Sounds like me on a good day,' he mumbled, wincing as Sheppard let out another torrent of abuse at those trying to calm him.

'I could admit you, too, if you're worried,' Keller suggested.

Rodney frowned at her. 'That was a joke,' he sighed, wondering how she could have missed that.

'Oh, right. Of course. Very funny,' she said, tossing him the briefest flicker of a smile. 'Now, if you don't mind – we're pretty busy here. Can someone get me a dose of Benzodiazepine to knock this man out! '

She made as if to steer Rodney toward the door, but he side-stepped her touch and headed towards Sheppard.

'Sheppard...Sheppard, it's me...McKay.'

Sheppard's head snapped up from the bed. 'McKay. Don't believe them. I'm not sick. They're Replicators...maybe all of 'em! Don't let 'em sedate me!'

_Okay, maybe Keller has a point!_ McKay pondered,knowing there had been no sign of an Asuran vessel approaching the city at any time.'I think you need to get some rest, Sheppard. All this has been a bit too much for you. You should let the doctors help you,' he said, speaking slowly and clearly to be sure his friend would understand.

Sheppard's green eyes flashed with annoyance. 'Don't patronise me, you arrogant little –'

'You need to go, Rodney,' Keller advised him, raising her voice over the colonel's insults. 'I think he's finding your presence here...disturbing.'

'I'd say he's finding just about everything disturbing,' Rodney replied, his eyes bulging at the sight of Sheppard straining against his cuffs. It was a good thing they were thickly padded because he suspected the colonel wouldn't have stopped even if they were slicing his skin to ribbons. As it was, they were rubbing his wrists raw already.

'All right. Would you tell him I'll be back to see him later...once he's a bit more rational.'

'Of course,' she nodded, turning away to attend the beleaguered military man.

As he shuffled his way out of the infirmary, Rodney felt eyes burning into him all the way to the door. He glanced back over his shoulder to find Ronon glaring after him. Very slowly, a smirk curled the Satedan's lips, then he looked away, returning his attention to battling the colonel.

Rodney felt a shudder run the full length of his spine. Something about that smile was incredibly unnerving. The Satedan did have a somewhat cruel sense of humour, but even he didn't normally find Sheppard's suffering amusing. They were almost like brothers, unerringly protective of one another. Why would Ronon behave this way now?

Unwilling to challenge him on his odd behaviour due to his innate fear of pain, Rodney continued on to his lab. He didn't need a pick-me-up now; seeing Sheppard in that state had definitely been the wake-up call he needed. But he didn't have time to worry about everyone else. There was still a lot of work to do on Elizabeth's nanites if he hoped to get them in line and stop them adapting any further.

*****

Three hours and six cups of coffee later, Rodney continued to work with trembling hands, now completely wired on caffeine and power bars. His brain was tired but functioning well, at least as far as he could tell, yet the solution to the nanite problem still eluded him. Even Zelenka had given up on the challenge, telling him he had other things to check. It should have been complex but doable, but the more Rodney tried, the more the damned things seemed to lock him out. They appeared to be permanently stuck in the programming he'd provided to save her life after the accident, and now wouldn't allow him to alter them. The only changes possible were those they made themselves to protect her well-being.

There had to be something wrong in the way he'd written the program. He couldn't change them, yet they were adapting on their own. That was way beyond what he wanted them to do, and pretty scary considering what the Replicators were capable of.

Rubbing his tired eyes, he sat back and stretched, then scratched his ribs and straightened out his aching knees. All this sitting around staring at computer screens was crippling him. What he wouldn't give to be forced to have a stay in the infirmary...no, he reconsidered, remembering the treatment Sheppard had been undergoing when he'd last seen him, maybe not. A few hours in his own bed were definitely preferable to that.

Giving himself a second or two longer to rest his eyes, he got back to the nanite code, this time noticing something he hadn't seen before. It seemed obvious now when he looked at the screen, but one of the decimal points was a fraction larger than the others. Since it was the only anomaly he'd found, he figured he'd better correct it...though he couldn't imagine how the computer had changed the size of the text for one character. It was probably something Zelenka had interfered with earlier and nothing to do with the problem he was trying to solve.

Highlighting the error, he tried to delete and replace it, but found it wouldn't go. He tried again, three times, but the persistent dot would not budge. 'This is nuts,' he muttered to himself, deciding to stop wasting his time on the shortcut, and write in the instruction in a way the damned thing couldn't ignore. This time it didn't ignore it, but the instruction didn't do quite what he planned. Instead of disappearing, the decimal point expanded out into reams of data, spooling down his screen so rapidly he had no hope of keeping up with it.

'What the...' he breathed, as his eyes tried to lock onto anything whizzing past on the screen. He couldn't define anything specific in the way of instructions, but he could see it was Asuran, not the re-written coding he had created. 'Oh, this is bad...this is very bad.'

'What is bad, Rodney?' Teyla asked, taking him by surprise since he hadn't heard her enter the lab.

Surreptitiously angling the screen away from her, he covered the problem as best he could. 'Oh, I'm still getting nowhere with the nanites, that's all,' he lied, wondering why he felt compelled to be dishonest with her. Was he really going to let Sheppard's inane ramblings in the infirmary colour the way he treated his other friends?

'I do not think it is necessary for you to keep working on that problem when your skills could be put to good use elsewhere,' Teyla suggested, a hardness to the way she looked at him he'd never noticed before. A shudder ran up his spine again. Why would Teyla think leaving the nanites active inside Elizabeth was a good thing? She'd wanted them out of her as much as he had not a day ago.

'Er...yeah...you're probably right,' he agreed, closing the lid of his laptop. 'There are plenty of other systems that could use my magic touch.' He wiggled his fingers as he said that, but Teyla only arched her eyebrow as if she had no idea why he would do such a thing.

'That was me doing magic...you know...like a magician...I've told you about magicians before, right?' he said with a pained grin.

Teyla ignored the question. 'Sheppard has been setting your priorities for the past few days. Considering what has now happened, I think it would be wise to review operations and re-evaluate what is most needed.' Her eyes drifted around the room, finally stopping when they fell on the ARG resting on a workbench nearby.

'Well...I know Sheppard has gone bye-byes for the time being, but most of what he asked me to do actually made sense,' Rodney told her, feeling the need to defend the absent colonel.

'We will decide that now.'

He gaped back at her, troubled by her firmness. 'Who exactly is this 'we'?' he asked.

'Major Lorne and myself. We feel that if the responsibilities are shared between two of us, in the way that Dr Weir and Colonel Sheppard shared them, the pressure will be more bearable.'

'Okay, I can see the sense in having a dual leadership again, and Lorne is the obvious choice for military commander, but who decided you should join him?'

'You can think of someone more suitable?' she asked, narrowing her eyes in a way he could only interpret as menacing.

'No...I just thought the IOA might want a say in all this.'

'I am more than qualified to lead people than most in this city. Would you rather do it yourself?'

He shook his head. 'I...I didn't say that...'

'I'm sure you realise your skills lie elsewhere, Rodney. Much as I am certain you would make a good leader, you are a far better scientist than I could ever be.'

'Well, yes...how's Sheppard doing?' he asked, changing the subject.

'He is...as well as can be expected. Dr Keller is keeping him sedated for the time being until his mind is more settled. I fear it will take some time for him to recover his senses fully.'

'You really think he's that bad?'

'Dr Keller believes he is quite insane, and if I am honest, I would say I have seen this coming for some time. Sheppard carries so much guilt within him...a man can only bear so much.'

That didn't sound like the Teyla he knew. First, she'd told him to stop working on the nanite problem, now she seemed determined to undermine Sheppard's authority. Those were two things he would never have expected to hear from her.

'Well...I've got a thousand other things I need to be doing,' he said, hoping she would take the hint.

'That is all right, Rodney,' she said, resting her hand on his. 'Major Lorne and myself need to contact the IOA and give them an update on the change in circumstances following Colonel Sheppard's...indisposition.'

'Good, good...you run along and do that then!' he said, snatching his hand back and grinning almost maniacally. She eyed him oddly, glancing momentarily at the ARG once more before making her way out of the lab.

McKay let out the breath he'd been holding for the last few seconds in one huge sigh. Sheppard had been right; there really was something weird going on with Teyla. He'd never seen her behave that way before, and he'd never once known her to have a bad word to say against Sheppard. But the colonel had said they were Asurans, surely that couldn't be right?

Checking no one else was nearby, he began to reprogram the sensors to pick up the energy signature of Elizabeth's nanites. It took a few minutes to do it, then he sat back and watched his screen, waiting for the results.

The scan picked up Elizabeth first, as she was the strongest source of the units, then he knew the samples in the lab and the infirmary would show up, too. What he didn't expect were the dozens of other dots suddenly popping up all over the city, some of them quite faint as if only a few nanites were present, others much more substantial. But the really scary thing was that new dots kept appearing every few seconds. The infection was spreading through the crew as he watched in open-mouthed horror.

'Oh crap!' he gasped. 'He was right...well, kind of. How the hell did this happen?'

An alarm sounded on the laptop beside him. At first he ignored the persistent and somewhat shrill beeping because he was so enthralled by the saga unfolding on the screen. Then, the noise wheedled its way into his screaming brain, forcing him to acknowledge it. It was the disruptor frequency program; it had found something.

McKay spun the laptop round to face him, frantically studying its findings. He ran the frequency through the numerous simulations he'd set up, including one with the most up to date information gathered from Elizabeth after the nanites began to act on their own initiative, and each time it was successful.

'Ha!' he barked, his face erupting into a victorious smile. 'I did it. I actually did it.'

But there was still a problem. If Teyla and Lorne, and, come to think of it, everyone else likely to be manning the control room were already infected, it was highly unlikely they would let him in there to replace the city's shield crystal with the re-programmed ARG control crystal and do the work he needed to carry out to make the disruptor work. So what now?

His eyes darted about the lab as he tried to think of some way of getting to the shields. He supposed he might be able to carry out the reprogramming necessary to accommodate the crystal and it's function from another terminal in the city, but it might be detected, and he still needed to swap over the crystals.

As he tried to think of some distraction that might divert attention from the shield systems, his eyes finally came to rest on the tablet with the jumper diagnostics he'd been running since accessing the remote systems. A jumper! He could do the same thing he'd done on Asuras, except that had been a relatively small field, and that was all the power source on the jumper had been able to manage. Of course...there were ways of augmenting power systems, and it wouldn't take _that_ long...not for a genius like him. All he needed was a quick burst of power that would last long enough to sweep the entire city in one go. So, he had to get the reprogrammed ARG crystal and a naquadah generator into a jumper so he could set the field off throughout the city.

Wracking his brain for where he could find a naquadah generator no one would miss, he remembered a project one of his team had been working on prior to all the problems of the past several days. He was pretty sure no one would check it for the next few days because everyone was busy repairing the city, so he could grab that one with little difficulty...theoretically.

Half an hour later, Rodney was sitting in the pilot seat of Jumper One. He'd attached the naquadah generator to the power relays, taken readings to ensure it was generating enough energy to help the shield spread, and was now finalising the instructions of what the ship's shield should do once activated. Unlike on Asuras, where he'd needed the shield to simply extend downwards, here he needed it to extend in all directions, encompassing the whole city and everyone in it in a matter of seconds before the Replicator nanites could adapt. He'd just keyed in the final codes when he heard a voice in his earpiece.

'What are you doing, Rodney?'

It was Zelenka.

'Er...nothing much...why?'

'I thought you had already accessed the remote commands for this vessel?' Radek asked, now walking up the rear ramp and planting his hands on his hips as he waited for an explanation.

'Well, I was just checking them out again before doing a test run...what do you want, Radek?'

'I'm having difficulties with the city's shield. As you know, it was up and running and fully extended, but the whole thing now appears to be collapsing.'

'What...collapsing! How is that possible?'

'I don't know, Rodney. That's why we need you to look at it.'

'So you have absolutely no idea what's gone wrong...I thought you were supposed to be smart!'

'Well, yes...but not as smart as you.'

It suddenly occurred to Rodney that Radek should have had some idea what was happening with the shields, and would never have dared to come before him claiming to be so clueless. And he also realised the Czech was standing on board the jumper, and as such would not be caught by the expanding disrupter field. He had to get Radek off the jumper, run some simulations, and then set the damn thing off. He couldn't afford to be found out, and he couldn't afford anything to go wrong.

'Okay...you go on ahead and I'll catch up with you,' he said, hoping to rid himself of the diminutive scientist long enough to make sure everything was as it should be to set off the disrupter.

'Teyla asked that you come now...I really think you should, Rodney. We can't afford to be without the shield for long.'

_Dammit! _Apparently, Zelenka was determined not to leave him working on this project. Did the nanites inside him somehow sense when something was a threat. Glad the Czech hadn't seen him inserting the ARG crystal into the jumper's systems, Rodney figured he was going to have to humour the man and sneak back later.

'All right, fine. I'll come. But I swear if it's something obvious I'm going to demote you.'

'Whatever you think, Rodney. But you must come right away.'

McKay shutdown his laptop, but left it on the pilot seat, keen that everything should be there for him to run a simulation the moment he could break away from the shield repairs.

'You know, you probably shouldn't bother with the jumper amendments considering Colonel Sheppard has been declared unfit for duty,' Zelenka said as they walked.

'Oh, this from the man who was willing to believe anything he said yesterday,' Rodney blustered back, keeping up the facade of their normal bickering.

'Well...obviously I was wrong about that. He clearly poses a danger to everyone in this city. It's essential he's kept out of the way while we work.'

'Yes...yes,' McKay nodded, seeing through their transparent ploy so easily now he wondered how he could ever have fallen for it. 'He's completely lost the plot, poor guy. Good thing Lorne and Teyla are in charge now. Things should start improving around here soon.' He could feel little rivulets of sweat breaking out on his forehead as he strained to maintain both the ruse and his nerve. He was a terrible liar, always had been; he wondered how long he could keep it up.

As they were passing the labs it suddenly occurred to him that he appeared to be the lone free-thinking person still able to move about the city. That meant if he went to the control room he would be surrounded by infected people with little chance of getting away from them to carry out his plan. And suddenly, the thought he was the only one making that stand was terrifying for him. He was a scientist, and fighting still wasn't something he felt comfortable with on a physical or ethical level. Sure, he could push it down when necessary, but the fear always surfaced, no matter how hard he tried to keep it down. Sheppard, Teyla and Ronon were naturals, able to mentally detach themselves from the deeds they had to do to ensure their success. But the obstacles he might come up against were all people he knew, at least by sight even if he couldn't remember their names. He wasn't sure he could do what it might take to get back to the jumper bay if any of them stood in his way.

But there was someone who could.

Making a big show of rubbing his forehead, he stopped walking. 'You know, Radek. I have a terrible headache. I think I might head over to the infirmary and get something for it. Why don't I meet you at the control room when I'm done?'

Radek raised his eyebrows, but didn't question him. Perhaps headaches were a good sign as far as the infected personnel were concerned. 'Okay, Rodney. But no sneaking off to finish working on that jumper. We need you fixing the shields.'

'I'll be right along,' Rodney promised, grinning inanely as he watched Radek shuffle away.

Once he was around the corner, Rodney bolted back toward the lab. He needed Sheppard, but to reach him, he had to use one of the colonel's own ideas. If only he'd been as willing to listen when the colonel had first asked him to do it those several long days ago.


	22. Chapter 22

_The jumper banked to the left and swept down low above the ocean. Sheppard kept the coastline in sight the whole time, figuring he did he could bring the jumper in to land should something unexpected happen. His team sat tense in the cockpit with him, faces taut with worry._

_'You picking anything up, Rodney?'_

_'Nothing,' the scientist called back to him. 'Are you sure you saw a city ship approaching the planet?'_

_'Absolutely!' Sheppard spat. _

_'Are you certain, John? You have been under considerable strain lately...perhaps you simply dreamt it,' Teyla said, sympathy burning bright in her eyes._

_Sheppard didn't want her damned sympathy; he wanted her to trust him. Teyla had always trusted him...until now._

_'I know what I saw,' he growled. 'They're here somewhere...we just have to find them.'_

_'Oh, God!' Rodney suddenly gasped from behind him._

_Sheppard knew that sound. It meant he'd found something bad. 'What is it, McKay?'_

_'They're...they're under the water, they're right below us!'_

_'Let's get out of –'_

_He couldn't even finish the sentence as he felt himself ripped from the pilot seat by Ronon's strong arms. 'No point, Sheppard. They're coming. Stop fighting and let it happen.'_

_The Satedan threw him to the floor, Teyla joining in to pin him down._

_From the corner of his eye, he saw Rodney jump into the pilot seat and try to regain control of the vessel. 'What the hell are you two doing? Let him up! We're gonna crash!'_

_Sheppard struggled against the hands holding him. 'Pull us up, Rodney!'_

_'I'm trying,' McKay yelled back. Then, more quietly, he breathed, 'Oh no!'_

_Sheppard now saw what had wrenched that final comment out of him. A tower just like the control tower of Atlantis was rising before them, shooting up at such speed there was no hope of the jumper pulling up in time. _

_He tensed, preparing for the impact..._

_'Yeh need to wake up, son. Atlantis is countin' on yeh.'_

Sheppard woke with the weirdest sensation he'd had a heavy drinking session and was now suffering the freakiest hangover ever. The ceiling seemed to sag down toward him as if the city were melting. Then, it retracted as he tried to focus on it, and repeated the motion several more times like some huge diaphragm shifting as Atlantis drew in laboured breaths.

Some distance away he heard a voice say, 'Oh, thank God! You're awake!'

Someone caught hold of his arm, pulling him up, and he had to grab on tight to the bed to stop himself falling off it. It was Rodney, and he was right there with him, his face blurring in and out of view. Sheppard felt as if his eyes were rolling around in their sockets, and the room swayed and tilted disconcertingly as if in confirmation of that fact. When he looked at his friend again, he could see Carson standing just behind Rodney's shoulder.

'C...Carson?'

'What? No! It's me, McKay. Sheppard! Sheppard! I need you to listen to me, this is very important,' he heard Rodney's distant voice screech, as if passing through wads of cotton wool.

He looked at the scientist, his face morphing and changing into twisted versions of all the people he knew on Atlantis before his eyes. He threw his friend a goofy smile. 'How'd you 'spect me to concentrate when you keep pullin' faces like that?' he asked, chuckling into his chest. 'Who else d'you do?'

'Dammit! I knew I'd get the dose wrong. We are so screwed!'

Sheppard felt something warm and slightly clammy grab his cheeks and hold his head still. It didn't stop the room from tilting...or was it him listing? When he managed to smack his forehead into the constantly changing face in front of him, he realised which one it was.

'Owww...Sheppard, I gave you some amphetamines to wake you up, but I think I over did it. I need you to focus on what I'm saying, not what you're seeing. Can you do that?'

'Sure...but do you do requests?'

Rodney/Ronon/Keller sighed despondently, the scientist's real face finally coming back into sharp focus as Sheppard's confusion began to lift. 'Please, Sheppard. I really need your help. Atlantis is in BIG trouble and I can't save it without you.'

As the stimulants won the fight for control of Sheppard's mind, his concentration made a huge jump in the right direction. 'Whassup, Rodney?'

McKay almost collapsed with relief, his whole body sagging as he realised Sheppard was finally paying attention.

'You were right to be worried, Sheppard. People _are_ acting weird, but they're not Asurans. Somehow, Elizabeth's nanites are spreading around the city, infecting everyone they come in contact with. They're still human, but once the nanites replicated to optimum numbers, they're falling under their control.'

That snapped him out of his daze, adrenalin now coursing through him and helping to counteract the effects of any sedative still lurking in his system. 'And Elizabeth?'

'I don't know. She was in the isolation room when I scanned Atlantis, but when I tried to check on her on my way here, she wasn't there. Someone let her out.'

'Dammit!' Sheppard looked down at the bed beneath him, seeing the cuffs and straps now lying empty and idle. They'd pinned him down because they knew he was onto something. They'd realised he would try to stop them, so they'd shut him up and tried to undermine him until his nanites took over and meant he would do what they wanted. Well, they weren't going to get the better of him. He could still stop them...somehow.

'Wha's the plan?' he asked, his voice sounding louder to him now, but still decidedly slurred.

The scientist's face brightened at the question. 'You're gonna love it!' he grinned nervously, checking all around him. 'My program to find a new frequency for the ARG worked...right after I scanned the city and found out the place is riddled with nanites. What're the chances, huh?'

'Apparently, a lot slimmer than you'd think...' Sheppard mused, the nagging pain of his concussion just beginning to kick in behind his eyes again, although it seemed somewhat cushioned this time. Whatever Rodney had dosed him up with was making him feel pretty good now the weird initial effects had worn off. Right now, he was beginning to feel like he could take on the Asurans single-handed.

'Huh! I suppose so,' Rodney replied, looking surprised by the acuteness of his answer. 'Anyway, I reprogrammed the ARG crystal, but I couldn't get it to the control room because the place is swarming with infected personnel. So, thinking on my feet, I realised the jumpers are pretty central to this city, and at just about the highest point. So, I replaced one of our jumper's shield crystals and connected up a naquadah generator to give the power a boost. I've programmed it so it'll generate a disruption field big enough to sweep through and encompass the entire city. I was going to run a simulation to check I'd got the calculations right when Radek interrupted me. He didn't seem overly concerned with what I was doing, but he said he needed my help with the shields and I didn't dare refuse. I didn't want him hanging around the jumper and finding out what I'd been up to. So I said I would go to the control room with him, then I pretended to have a headache and came looking for you. I figured the two of us working together would have a better chance of pulling this off, right?'

Sheppard nodded. 'As long as Radek didn't double back and pull the jumper apart.'

Rodney's face froze in an expression of abject terror. 'Oh, God! I hadn't thought of that.'

'Forget I said it,' Sheppard ordered, realising his mistake now while Rodney slipped into shock in front of his eyes. 'Hopefully they have no clue what you plan was.' _Way to go, John!_

'But I never even thought of that. I should have brought the crystal with me. Why didn't I? It's so obvious!'

'Because you're panicking, Rodney. Now get a grip!' The scientist quivered in front of him, nodding but quiet at least. 'Chances are that crystal is still exactly where you left it, and that's what we're gonna assume. We can still do this.'

Though Sheppard knew it was mostly down to the amphetamines, he suddenly felt like he could run for hours, kick both Ronon and Teyla's asses at the same time, and figure out how to get the jumper fired up without any help from his present company. Thankfully, he remained rational enough to understand he needed to temper his responses because this was most likely their only shot at stopping the Replicators taking over and destroying the city.

He rubbed at his reddened wrists, remembering again how the infirmary staff had secured him to the bed on the premise of protecting him from himself. Clearly they'd all been acting under the influence of the nanites, but there had been a change of staff since then. So, where were those staff now?

'Rodney, where'd the medics go?'

'It's skeleton staff because it's night hours, so I took a chance and wheeled the EM pulse generator along here. The nanites haven't reached high enough quantities to be completely cohesive in some people yet, so the pulse is still able to disrupt them for a while. There's a few medics out there feeling a bit confused right now, but the nanites will soon reset themselves so we have to get moving. Oh, and I managed to sneak the amphetamines I gave you from the supply cupboard pretty easily. You know, they really should fit a better lock on that thing.'

Sheppard arched an eyebrow. 'I'll be sure to bring it up...if we survive this. But now we should haul our asses out of here before people start waking up. C'mon.' He leapt off the bed, and crumpled straight to the floor, his legs not quite in on the plan. He peered up at Rodney, who looked completely horrified. 'Er...a little help here?'

'Oh...sure!' McKay helped to pick him up, then wrapped Sheppard's arm around his shoulders. 'Ready?'

'Ready,' Sheppard assured him, feeling more confident now he was vertical.

They didn't get far. They'd only taken a few steps when a young male medic appeared, blocking their path. 'Where'd you think you're taking him, Dr McKay? You know he's not fit to leave the infirmary. I'm going to have to insist you stay, Colonel Sheppard.'

'And I'm going to have to insist you step aside,' Sheppard growled. There was no way they were strapping him down to that bed again, not while he had any say in the matter.

'You really can't leave,' the medic insisted.

Sheppard pushed himself up from Rodney and stood alone, swaying slightly, but certain he could stay upright. He hoped his belief was accurate and not another amphetamine fuelled misconception. 'Get out of the way or I'll move you myself,' he rumbled, sounding as menacing as his slightly shaky vocal chords would allow.

'Sheppard!' he heard McKay hiss behind him. 'You're in no fit state –'

He thrust up a silencing hand and Rodney amazingly stopped speaking. That had never worked before...at least not instantly.

The medic smirked. 'You can't get past me. Look at you, you can barely stand.'

'Barely's all I need,' Sheppard told him, then launched his full body weight into the man, knocking him to the ground.

He landed a few punches before the guy started fighting back, frustrating him with the speed with which the bruises and grazes he inflicted began to repair themselves. The colonel felt a primal urge to hurt this man for what he represented, nothing more, but he couldn't do that effectively if he couldn't even leave a lasting mark. The medic managed to flip Sheppard off him and throw him to the ground, sitting on top of him and raining down a few punches of his own...until Rodney set off an EM pulse that rendered his nanites temporarily inert again. Sheppard swung a right hook at the confused man that put his lights out and he toppled right off him.

McKay dragged Sheppard up from the floor and hurriedly supported him through the door and out toward the nearest transporter. Dabbing at his bloodied lip with the back of his hand, he allowed the scientist to steer him from the room. 'Shouldn't we bring the generator?' he suggested, as the doors closed behind them.

'We could, but it'll slow us down, and it'll be useless against anyone with a high level of nanites anyway.'

Realising Rodney had a point, Sheppard decided leaving it behind was probably best. Steadying himself against his friend, he tried to pick up the pace. 'Okay. Let's get out of here before anyone else sees us.'

'Where are we going?' McKay asked, hurrying after him

'Your lab. I need you to tell me everything you know and kit us out with whatever we need to see this through.'

Sheppard allowed Rodney to guide him to the transporter, then insisted on standing on his own feet while Rodney ordered it to take them to the correct location. The fight had left him a little shaky again, but he was already regaining his strength.

The transporter doors opened and McKay stuck his head out to scout around. He pulled back sharply, shutting the door, but not sending the transporter elsewhere.

'Dr Biro's out there,' he explained. 'Hopefully she'll pass right by.'

She didn't. The doors pulled back and Biro gaped at them, surprised to find anyone lurking inside. Sheppard acted instantly, punching her hard in the face. She folded to the floor, completely unconscious.

'Well, I guess she's not infected – not badly, anyway,' Sheppard said, matter-of-fact.

'You knocked her out!' Rodney gasped, helping the wobbly but thankfully more stable colonel to drag her into the transporter and close the door on her. 'You couldn't think of another way of testing her?'

'Not off the top of my head, no. Besides, I'm sure she'd understand...under the circumstances,' Sheppard pointed out. 'I'll apologise later...if we make it through this.'

Feeling stronger all the time, Sheppard managed to jog into the lab in front of Rodney, ordering him to lock the door to stop anyone getting in to them.

'Now, bring me up to speed,' he ordered.

Rodney brought up the date he'd unlocked from Elizabeth's nanites so Sheppard could see the extent of the problem. 'When I was studying the nanites from Elizabeth I found what looked like a minor anomaly in the coding, so minute I almost missed it. When I tried to delete and re-enter it, it turned out to be a microdot...you know...masses of compressed information. I didn't have time to read it all, but it was clearly Asuran in origin. I'm thinking they wrote it into her code when they took her prisoner.'

'But she said they didn't do anything to her...that they just asked her questions.'

'She probably has no memory of it now. Like I said, the data was compressed...and she did say they knocked her out for a while.'

John felt bitterness rising inside him. He wished Oberoth himself was here so he could let him know just what he thought of how he'd used Elizabeth to trick them. He would gladly punch his ugly metal face until he couldn't repair himself anymore. Realising that was more than likely the drugs talking, he pushed the thought to the back of his mind and tried to concentrate on what needed to be done.

'It's like the Greeks and the Trojans,' Rodney sighed.

Sheppard gave him a puzzled look. 'How so?'

'Well, the Greeks tried to get over or through the walls of Troy for ten years. Realising they couldn't, they decided to trick the Trojans into thinking they were giving up and got their finest artists to sculpt a horse to leave behind as a gift for a battle well fought. What the Trojans didn't know was that the Greeks hid thirty men inside the horse, who snuck out once everyone had gone to bed and opened the city gates to let the Greeks in.' He stopped, his jaw slackening as he realised what he'd just said. 'That's what this is about. They want someone here who will open the 'gate to allow them to get through.'

'And that's why we have to stop the spread of nanites here,' Sheppard said decisively. 'Please tell me you put the crystal and generator in the jumper with remote capabilities.'

Rodney blinked at him, baffled by the question. 'I put them in the jumper with remote capabilities. Why, are you heading to the chair? I haven't even had a chance to test the system yet!'

'No, I'm heading for the jumper. _You're_ heading for the chair. We're launching a two pronged attack, that way, if I don't make it to the jumper, you still have a chance to set off the disrupter field.'

'But...but if you don't make it that would probably mean you were —'

'Dead, Rodney. Yeah, I know. Don't go all mushy on me now. I need you to stay focused.'

'Okay. I'm focused,' he nodded, visibly shaking at the prospect of what they were up against.

'I want you to get to the chair room and then trigger Atlantis' lockdown protocol. Then, I want you to open doors for me so I can get to the jumper bay meeting as little resistance as possible.'

'Okay...that sounds doable! Most people are in their quarters now anyway.'

'Good. But first, we need to do this.' Sheppard pulled out his penknife and took off his overshirt. 'Do you have some tweezers?'

'Sure.' McKay pulled a set from a drawer in his workstation and passed them to Sheppard, looking decidedly bemused. As he lay his forearm on Rodney's desktop, the inside facing upward, Sheppard heard the scientist squeak, 'What're you doing?'

'When that medic wakes up, his nanites are going to communicate to everyone receptive to his messages that we're up to something. So, when they want to find us, what's the easiest way to identify us in this city?'

'Our subcutaneous transmitters,' McKay replied, a kind of resignation now tempering his tone.

Sheppard winced as he sliced through the outer layers of his skin where he knew the transmitter to be, finding an edge and then using Rodney's tweezers to tug it out. He set the tiny chip down carefully on the workstation so he didn't damage it, then wiped the blade of his knife on his trousers and passed it to Rodney, handle first.

McKay grimaced, and Sheppard could feel his patience wearing thin. 'This is no time to get squeamish about infection, Rodney. Just do it!'

'It...it's not infection that bothers me...' he said quietly, and John realised it was the thought of inflicting pain on himself that was turning his stomach.

Sheppard grabbed his arm and swiftly slit the skin where the faint scar from the device's implantation still showed. He pulled out the transmitter, placing it next to his, then made them both makeshift bandages from his shirt. 'No point in leaving a trail of breadcrumbs, right?'

Rodney shook his head, still clearly hurting more than he could deal with.

'C'mon, Rodney. Grab what you need, and let's get moving before they find us here,' Sheppard grunted, urging him into action.

Nodding and pressing his left arm to his chest to ease the pain, Rodney grabbed his laptop and tucked it under his other arm. Then he stopped, his face suddenly ashen. 'Oh my God, oh my God, oh my God!'

Sheppard halted. 'What. What is it?'

'I'm already infected. Teyla touched my hand the last time she was here in the lab. I got so carried away with everything else that I completely forgot –'

'How long ago?'

'I don't know...maybe an hour or so!'

'Well, I –'

'Oh my God. We're screwed!'

'Rodney!'

'No – we are. We're screwed! Any minutes now I could turn into one of them.'

Sheppard grabbed his upper arms and squeezed tight to snap him out of his ramblings. 'Snap out of it, McKay. I was pinned down by a whole bunch of infected staff hours ago, and I'm still fine. It takes time for them to replicate enough to take over the host, right?'

McKay nodded, giving a slight whimper.

'Then there's still a chance and we're against the clock, so you need to stop panicking, and start moving.'

'Yes...yes your right. Although, my head _is_ aching now –'

Imagining that was more down to Rodney's hypochondria than anything else, Sheppard urged him on. 'C'mon, Rodney. Stay positive.'

He led the way to the door. As they left, Rodney entered a locking code in the door controls. 'That should hold them for a while so they won't know it's just our implants in there. Once I'm in the chair I can control the doors and other things from there.'

'Good thinking. Now, you just do your best to give me a clear run at the jumper bay, and I'll do the rest,' Sheppard promised.

As he was about to go, Rodney spoke again. 'I'm sorry I couldn't fix Elizabeth's nanites, Sheppard. I really thought I was doing the best thing when I activated them...now...now I realise I was wrong.'

Sheppard paused, giving him a grim smile. 'I guess sometimes things are too broken to be fixed. We just have to learn to accept that.'

'I guess so,' Rodney agreed, for once humble in his response.

Regrets expressed, they left the lab behind and headed out in different directions. Sheppard took it cautiously, hoping Rodney was doing the same. Neither of them had any defence against the nanite-infected crew, not that any Earth weapons could do much to slow them anyway. They had to survive on their wits alone. Hopefully, the nanites wouldn't take hold before they could see this through.


	23. Chapter 23

Picking his way down several corridors, Sheppard made good progress even without Rodney's help, ducking into niches and behind architectural protuberances to conceal himself from discovery. The Ancients had thankfully expressed a preference for sculptural designs in their buildings, and though he'd often thought them somewhat over elaborate for their needs, he had to admit they were proving pretty useful right about now.

Unfortunately, his luck ran out when he turned down the next corridor and saw Lorne and a team of marines heading his way. He turned and sprinted back the way he'd come, hearing them order him to stop and feeling the air prickle as a stunner blast missed him by inches and fizzled across the surface of the wall beside him. The lighting cells in that area sputtered and died, casting him in shadow, and allowing him to stick to the wall and slide away beyond a doorway, and not a moment too soon. The bulkhead door shut only a fraction of a second later placing a barrier between him and his pursuers.

Steadying his breath, Sheppard tapped his earpiece. 'I take it I have you to thank for closing the doors, McKay?'

'_Yes. I'm in position in the chair room. Where are you?'_

'Outside the botany labs.'

There was a slight delay, then McKay piped up, _'Found you. There are four life signs on the other side of the door ahead of you.'_

'Yeah, I know...your timing is impeccable,' the colonel told him.

'_You need to double back. I can get doors open to get you around to the other end of that corridor without you having to encounter anyone else.'_

'Okay, sounds good.' Sheppard headed away from the doors, each new set yielding to him on his approach. His head was buzzing, more alert than he'd ever felt it. It wasn't exactly a problem, but was disconcerting all the same. He'd always been sharp in combat – able to judge situations, change plans, ignore orders – whenever he felt what he'd been told to do wasn't in everyone's best interest. Now, he felt like he could truly feel the menace around him, the danger lurking behind each door and wall, the anger of the tiny units desperately trying to avenge the acts of the Ancients and now of humans, too. He supposed, when you rationalised it, their behaviour wasn't entirely without foundation, but he didn't want to get too philosophical about it right now. At this moment, they were the enemy, and they were trying to kill everyone in the city; that was all he needed to know.

'_You can take the transporter in the next corridor on your left to get you up to the jumper bay floor,'_ Rodney said in his ear.

'Understood. You start accessing the jumper controls from the chair, that way, if I need to tell you to get things moving we won't lose any time.'

'_Okay...hang on...oh no, no, no. I...I can't lock this one out!'_

Sheppard stopped in his tracks, frozen by the fear apparent in Rodney's words. 'What is it, McKay?'

'_Someone's on the move...it looks like they're following your life signature and the doors don't seem to be a problem for them. Whoever it is, they're just overriding the controls and walking on through. It's like they have some kind of in-depth knowledge of how our codings work.'_

That suggested it might be one of the scientists. Rodney had mentioned Zelenka was under nanite influence; perhaps he was planning to check out what he'd done in Jumper One. Sheppard picked up the pace. 'That isn't what I want to hear, Rodney. Where are they?'

'_Approaching a transporter. It'll bring them onto the jumper level about the same time you get there, but they have to walk further. If you're quick, you should be able to set the disrupter off before they get there.'_

'Understood.'

Sheppard now gave it everything he'd got, tucking his head down and running into the transporter so hard he couldn't stop without slamming his shoulder into the back wall. He told it where to go and rolled his shoulder to ease the pain, not that it would slow him.

As the doors opened just outside the jumper bay he asked Rodney for an update.

'_Whoever it is will be at the transporter any time. You need to work fast.'_

Jumper One was on the upper level, so John ran to the first set of steps and began to mount them, three at a time. His body felt faster than ever, his heart pumping and his mind racing through what he had to do. He had to open the rear hatch and get that weapon activated before whoever was on his tail stopped him. In seconds, he made it across the metal gantry to the second set of steps and started up them.

'_Sheppard. Are you there yet because –'_

A shot rang out, hitting the step just behind him. _Crap. _He kept going, but another shot zinging past his ear and grazing it knocked him off balance. He fell down the set of stairs he was climbing and lay at the bottom of them, stunned into inactivity. The view of the jumpers swam around him, tauntingly close, but just out of reach.

Footsteps crossed the floor below and he knew he was in trouble. 'Rodney...you have a go.'

'_What...what's happening?'_

'Just do it!' he croaked.

John twisted his head round to see not Zelenka but Elizabeth approaching on the level beneath him. Even that simple movement caused immense pain in his neck, and he knew the sensible thing would be to stay still and hope Rodney fixed things from his end. But when had he ever done the sensible thing when lives were at stake?

He rolled onto his knees, getting to his feet just as Rodney confirmed the worst.

'_Sheppard. I can't get the jumper up. Someone's disabled the remote link. God...I can't concentrate...I...I can't figure out how to fix it!'_

'Rodney...Elizabeth's here,' Sheppard replied by way of an explanation and encouragement for his waning friend.

'_Elizabeth? Oh God. Are you all right? Can you get to the jumper?'_

'That's a negative,' Sheppard advised him, feeling a warm trickle running down the side of his neck from the slight wound she'd inflicted.

'_All right. Leave it with me...I can do this...I can do this!'_

Rodney's confusion didn't make sense. The colonel knew he'd been exposed to the nanites a number of hours before his friend, and he still wasn't feeling the effects. He seriously hoped it was just another case of Rodney panicking before performing the necessary miracle.

'I need you to come back down to my level, Colonel Sheppard,' Elizabeth said calmly, still aiming the 9mm she'd fired at him.

He swallowed hard and thought about complying, then figured he had nothing to lose. 'Why don't you come up here? I'll take you for a flight.'

'I suspect that would be very bad for me,' she smirked. 'Dr Zelenka closed down the link between the chair and the jumper, and I thought I should come along and investigate what Dr McKay was so intent on doing here. Funny, I thought you and he were still in the lab or I would have brought reinforcements. Maybe I should send them along to the chair room instead. I take it that's where they can find him.'

Hoping to deter her from doing that, Sheppard asked, 'What's the point? Rodney can't do anything without remote access.'

'I expect Dr McKay is working on that problem already since he's not fully under our control yet. So, what will I find when I get up there, Colonel?'

'I don't know. Why don't we head up there together and take a look together?' he suggested. He had to get into that jumper, no matter what the cost.

'You are not getting on that ship,' Elizabeth growled, fixing him with a piercing glare, and raising her gun so it was aimed at his head. 'Now, I will ask you once more, please come down to this level.'

'_Colonel, I've checked out the remote access and I think I can fix the link, onus on the think, but I...I need five minutes. Can you give me that?'_

'Affirmative,' he said softly, starting slowly down the steps to Elizabeth's level. He could feel the various knocks and scrapes his body had sustained in the fall as he gingerly dismounted and limped his way across to her. He stopped a good two arms' lengths away from her, watching her warily. 'I wondered when you'd make your move, Oberoth,' he said without a flicker of fear.

Surprise registered momentarily on Elizabeth's face, but was soon replaced by respect. 'Very clever, Colonel Sheppard. I take it you've been expecting us?'

'You could say that,' he replied, regarding his former friend frostily. 'I wasn't quite sure how or when you'd arrive, but I knew you wouldn't let us get away with stealing your ZPM like that.'

'We wanted you to understand true betrayal before you died, Colonel. You see, we discovered something very interesting about you from Dr Weir. You carry the strongest know genetic link to those the peoples of this galaxy call the Ancestors. The Lanteans wanted to destroy us when all we had done was try to please them. We did not deserve that treatment, just as I'm sure you don't feel you deserve this.'

Sheppard knew if he could keep the Asuran leader talking, Rodney would more than likely fix the problem slowing them down...as long as the nanites didn't kick in first. But what did you talk to a homicidal Replicator about? He decided to butter him up and get some more intel. 'I have to confess I'm impressed with how easily you found us. How'd you know where we jumped to?'

'Oh, Dr Weir wasn't as clever at hiding information from us as she thought she was. The nanites made sure of that.'

Sheppard felt weird listening to those words coming from Elizabeth's mouth. She _was_ Dr Weir, and the fact this Asuran monster was controlling her mind and using her to destroy the very place she loved so much made him mad enough to tear the bastard limb from limb...not that it would do any good.

'I take it a lot more happened in those missing days than she remembers. Have fun tampering with her mind, did you?'

'Dr Weir proved a most formidable adversary in her time with us. She was always able to enforce a certain amount of will on her nanites, no matter what we tried to do with them. I would never have imagined a human mind could be so strong. We even threatened to remove the nanites if she did not comply, but that thought apparently held no fear for her. She views us as...inferior in some way.' She laughed, or rather he did, setting Sheppard's follicles to rigid attention.

'What's so funny?' he demanded.

'The thought that you 'humans' are in any way a match for us. You are weak minded and foolishly compassionate. Your inability to do what is necessary without over analysing the consequences and ramifications will be the end of you...at least in this galaxy. Perhaps, in time, we will succeed in wiping your scourge from the whole universe, and then we will know the Lanteans can never return.'

'The Lanteans are long gone, Oberoth. Elizabeth doesn't deserve this. She doesn't have Lantean genes, she didn't agree with the military strike on your planet, and she didn't come up with the idea of stealing your ZPM.'

'Yet she helped to carry out the plan. She sealed her fate the moment she stepped onto Asuras, Colonel. She gave herself up to save you, and now I intend to make certain she regrets that decision.'

A surge of nausea welled in Sheppard's guts as he realised what that meant. 'Is she...aware of what's happening?'

'Oh yes, Colonel Sheppard. I assure you Dr Weir's mind remains very much intact. The only way we could exert any hold over her was to open up a subspace channel and feed my own consciousness into the nanites replacing her injured brain tissue. I now have control of this body, and all the other nanites replicating their way through the crew of Atlantis, but she is also here.'

'How did you infect everyone?' Sheppard demanded, trying to keep the flourishing anger inside him in check. Anger was his enemy right now; he had to keep a clear head.

'That was courtesy of your friend, Teyla. She underestimated us...as you all did. You believed we could only be transferred by direct physical contact, but we found another means. I'm sure you would appreciate a more detailed explanation, but since I realise you are only trying to provide time for Dr McKay to repair the remote connection to the Jumper One, I find myself even more intrigued to know what is so special about it.'

As Elizabeth tried to side step him, Sheppard put a restraining hand on her shoulder. Though he didn't relish the thought of fighting her, he would do so if necessary. 'I won't let you go up there.'

Oberoth stared out at him through Elizabeth's intelligent green eyes, and, very slowly, a cruel smirk spread across her mouth. 'What makes you think you are any more capable of stopping me than anyone else in this city?'

'I'm not under your influence yet,' Sheppard pointed out.

'Aren't you?' she asked. 'Are you certain...or is it just that I have chosen to allow you to keep your free will for a time because I wished you to witness the destruction I plan to wreak?'

Those words sent a cold chill through the colonel's entire body. He hadn't even considered that prospect. He'd assumed he'd been infected since the spread was so wide, but had hoped the numbers of nanites inside him weren't high enough to take control yet. This was an entirely unexpected possibility. Hoping it was nothing more than a bluff, Sheppard left his hand exactly where it was.

'I won't let you go up there,' he repeated.

Elizabeth grasped his hand in a crushing grip, reminding him of the strength the nanites loaned to their host. 'Then allow me to take the decision away from you.'

An odd tingling passed through his body, and Sheppard realised he couldn't move. He struggled to will himself into action, sweat breaking out on his forehead from the sheer effort of trying to break the nanites' hold over him.

'You see, Colonel, as the strongest link to the Lanteans we wanted you to see what it was like to witness everything you'd strived for obliterated. But we infected you to be sure you could not stop us if you found out the truth of our plans. Your nanites will hold you still until I'm finished.'

Elizabeth began to walk away toward the steps leading up to Jumper One, and all he could do was scream after her. 'Elizabeth...I know you're still in there. Please, stop him!'

To his amazement, she came to a faltering stop. She was fighting. He felt the pressure that had built inside his own body suddenly melt away and he rushed forward, placing himself in front of her. When she looked at him, he could see tears in her eyes. 'Elizabeth...keep fighting him...we just need a little more time.'

'I'm sorry,' she whispered, pain registering in her face as she tried to maintain control. 'I don't know if I can.'

'Yes...yes you can, Elizabeth,' he told her. 'You're the strongest person I know. Rodney and I need your help. Atlantis needs your help!' Fully aware he was asking her to sacrifice herself for the sake of the city and everyone in it, the thing he had wanted to stop her doing in the first place when forced to leave her on Asuras, it took every iota of strength he had to make the request. He'd promised her she would get through this. Now he, too, was guilty of making a promise he couldn't keep.

She nodded, biting her bottom lip. 'If he manages to fix things, tell Rodney he did good,' she said quietly, pain scoring across her brow as the nanites in her head fought to reassert their control. 'And, John...'

He swallowed down a knot of emotion blocking his throat. 'Yeah.'

'You did good, too.'

As those words faded, he saw her eyes harden, and he knew she was gone. He hadn't even managed to say goodbye. That moment of regret distracted him as the blow came flying, and the butt of the 9mm made sharp contact with his temple, stunning him. He dropped to his knees, his world spinning.

'You will not defeat us!' he heard Elizabeth's voice tell him, the tone now much harsher and seething with pure hatred – Oberoth's hatred for anything and anyone of Lantean origin.

Sheppard felt the pressure building inside him again, weighing down his limbs and leaving him physically submissive while completely conscious of what was going on. He forced himself to concentrate on moving, to focus on what letting Oberoth take control of him meant. It meant the end of everything Elizabeth had dreamed of finding, fought to hold onto, and strived to nurture. She'd loved the place from the start, a love they'd all grown to understand and share. Everyone he considered his family was at risk. He wouldn't let Oberoth use her this way...even if it meant losing her. She deserved to be remembered for something more than destroying Atlantis.

He could hear the city humming around him, calling out for help as if it knew it was about to die, and he knew he had to save it. Though the agony of movement was almost unbearable, he set himself into motion, and once the nanite hold was interrupted, he felt instant relief. It was as if he had been set in concrete and someone had struck it with a sledgehammer to break him free. Oberoth had said Elizabeth wielded some control over her nanites. Well, if she could fight them, so could he.

Sprinting for the stairs he was soon behind her, grabbing her ankle to stop her progress. Again, her strength prevented him from halting her completely. Regaining her balance, she turned and fired at him, just missing his shoulder as he anticipated the shot and ducked away. He continued to hold her leg refusing to let go. _C'mon, Rodney, _he thought. _I can't stall her much longer!_

'Elizabeth!' he called, appealing to the friend he knew still resided in there somewhere. 'Don't let him do this!'

She turned to look over her shoulder at him, for a moment a flicker of emotion lighting them up with a familiar anxiety, the same fear he'd seen when Ronon had dragged him away on Asuras. Hope flooded through him; she was still battling. Then, she kicked him back. Sheppard slipped, precariously balanced on a step and hanging on by only one hand. Determined not to let her get the ARG crystal, he swung himself back towards the stairs, hearing a crack ring out just as his fingers tried to grasp and missed the rail.

In an instant his strength abandoned him. His limbs now useless rather than immobilised, the grip he had maintained slackened and he fell back.

His impact with the floor shook through every inch of him, and for a moment nothing registered other than the fact he was staring up at the retractable roof. What had caused him to fall? Had he lost his footing? Had Oberoth made the nanites somehow weaken him? Only after a few more seconds passed did he feel the burning sensation in his side. He clutched at it, feeling a warm, sticky dampness he found worryingly familiar beneath his hand. Lifting his head as much as he dared, he saw the blood now staining his fingers. His head fell back against the floor as his body protested at the effort required to keep it raised. He'd been shot. But Rodney still needed more time; he had to find the strength to move again, even if it was just to distract her long enough to shoot him again.

'_Sheppard...Sheppard! I...I think I've done it...at least I hope so. Is it safe to fire up the jumper?' _

Rodney's voice drifted through the haze of his pain and bloodloss and pulled Sheppard back from the shadows he was sinking into.

'Do it,' he croaked, craning his neck to see where Elizabeth was. She was only metres away from the jumper. 'Do it now!'

He heard the engines fire up and, a moment later, a gut wrenching cry. Elizabeth buckled and clutched the rail, and for a moment, their eyes met once more. In that exchange he knew it was his friend looking at him, and he hoped she understood how sorry he was for what she had come to. Then, as the effects of the disrupter field rippled through the city, the work the nanites had done to repair her began to unravel. Her hair fell away, falling gently like feathers to his level, and as blood dripped down from her opening wounds, her eyes clouded and she pitched forward, falling over the barrier and crashing to the floor just beyond his reach.

Her eyes, the pupils now fixed and dilated, stared at him. Lifeless. Hollow.

She was gone.

The jumper bay fell terrifyingly silent as an unnatural coldness crept through Sheppard's body. His head spun, probably a combined effect of the nanites suddenly shutting down and the various blows he'd taken to his head. Though he was tempted to just lie there and let the darkness take him, he knew he couldn't. The Asurans knew where they were. They had to move the city again.

Looking back at Elizabeth, he whispered, 'I'm sorry,' then rolled onto his knees and started to crawl toward the jumper bay door, activating his earpiece as he went. 'Rodney...Rodney! Are you there?'

His question met with another resounding silence, and for a horrible moment he thought something bad had happened to the scientist. 'Rodney!'

'I'm here...just gimme a minute to...wow...this feels so weird.'

'Yeah...I know what you mean,' Sheppard agreed, trying to keep the groan from his voice as a pain speared through his side. 'Your plan worked. Elizabeth's nanites have been neutralised...that's why you feel strange...I think.'

'_Is she...'_ McKay's voice faltered, unable to even finish the question.

'She's dead, Rodney. And so are we if we don't get the city moving again. The Asurans know where we are, and they know we've stopped their plan. Please tell me the hyperdrive is functioning.'

There was a pause._ 'No...repaired but deactivated. I can get it up and running pretty soon, though.'_

'Then do it, Rodney. And cancel the lockdown. I'll make my way to you.' He moaned slightly as he tried to move, hoping Rodney hadn't noticed.

Unfortunately, he had._ 'Are you...hurt, Sheppard?'_

'Just a flesh wound,' he lied, clutching his side as a wave of pain doubled him over. 'Now get the doors open.'

'_On it.'_

Crawling to the doorway, Sheppard pulled himself up on the frame. Glancing back one more time, he closed the jumper bay door behind him and put in his authority code to lock it. There was no way he would let just anyone stumble across Elizabeth looking that way.

Swaying toward to the transporter, using the wall for occasional support and leaving a trail of bloody handprints in his wake, he quickly got himself on the right level for the control chair. All around him confused crewmembers staggered out of doorways, leaned against walls, or sat wherever the dizziness of the sudden nanite shutdown had hit them.

Sheppard wasted no time checking on them. Their confusion would eventually pass, but if he didn't get Atlantis into hyperspace, wooziness would be the least of their worries.

Outside the chair room he found several dazed members of the crew, including Teyla and Ronon. Apparently Oberoth hadn't been joking about sending his acolytes to stop Rodney. As she looked up, his condition seemed to snap Teyla out of her daze. 'Colonel, you're wounded!' she gasped, jumping to her feet to offer him her support.

Ronon was soon on hand to hold him on the other side. 'What the hell just happened?'

'Long story, and believe me, we don't have time for it right now. Just get me to the chair.'

They did as he asked, supporting him until he was standing in front of Rodney, who still occupied the chair and worked furiously on his laptop. 'It's taking a little longer than I thought, but I should have the hyperdrive on-line in –' he glanced up, 'Jesus, Sheppard. You said it was a flesh wound!'

Sheppard looked down at the blood oozing out through his fingers and shrugged. 'It's all relative, I guess.'

'So Einstein said!' Rodney snorted. 'But I think even he'd struggle to apply the theory in this case!'

'Is the hyperdrive up and running?' Sheppard demanded, leaning heavily on the chair.

'I just need two more minutes.'

'Maybe you should let the colonel sit, Rodney. That way he can take command of the chair as soon as the hyperdrive is enabled.'

'Wha...oh, yeah. Sure.'

Sheppard slumped into the vacated seat, the chair tipping back and lighting up as he did so. 'I'm gonna get us moving while you finish up,' he told the scientist, firing up the Atlantis' engines. A shudder shook through the city.

'Where are we going?' Teyla asked.

'The second most viable planet Radek identified the last time we needed to jump,' Sheppard grunted, grimacing as the pain in his gut redoubled with the effort of powering up the city's engines.

'_Colonel Sheppard? Is that you?'_

Chuck's strained voice broke through on Sheppard's earpiece. 'This is Sheppard,' he replied. 'We're moving the city. Alert all personnel.'

'Sir, a Lantean class city ship has just emerged from hyperspace and is approaching our position. They're firing drones.'

_Damn it! _'Rodney?'

'Almost there,' the scientist snapped.

'The shield'll protect us, right?' Ronon grunted.

The city shook with the impact of two drones hitting one after the other. 'I'll take that as a no,' Sheppard replied grimly.

'Dammit. Radek wasn't kidding about the shield being down. I have to reactivate it before we can make the jump,' Rodney told them.

'Anytime now would be good, McKay,' Sheppard growled. The city began to lift, but the sheer effort seemed to drain him and he lost concentration, the engines faltering.

'You are in no condition to do this, John,' Teyla gasped, gripping his arm.

'So tell me who else can since half the crew don't even know what day of the week it is?' he barked back at her, his voice betraying how scared he was. He bit it back. 'I can do this. McKay, you just get me shields before they take out the engines.'

He turned the city, the force of the movement throwing everyone off balance.

'How am I supposed to work when you do things like that?' McKay demanded, glaring at him from his position on the pedestal.

'I'm trying to keep us alive, Rodney. Do we have shields?'

Another impact told him the answer.

'Almost there,' McKay promised. 'You just keep us moving.'

Everything around them vibrated violently as the city continued to climb. Sheppard wasn't sure if it was just the chair shaking or if he was shaking independently of it. The wound in his side throbbed with a growing intensity, the blood flowing out quicker with his increased heartbeat and breathing. An unhealthy chill had him in its grip, making him feel like he had ice water in his veins rather than blood. He had to stay conscious to get them through hyperspace. As he concentrated, he sensed the shields rise, and the next impact sounded like nothing more than a distant thud.

Confident they could now rise safely out of the atmosphere, Sheppard took the city higher, knowing he had to gain altitude before they could make the jump. 'The hyperdrive's on-line. Just a few hundred feet more and you can activate it. All you have to do is set us off and the city will take us there,' Rodney told him.

Sheppard screwed his eyes shut and willed the city to move faster. He could feel the pull of oblivion tugging at the edges of his consciousness, the twin gremlins of bloodloss and exhaustion waiting to claim him. All the time Teyla's reassuring grip remained on his arm. She had always been his rock – his constant in a universe that insisted on almost constantly throwing him curveballs. Elizabeth might be gone, but the rest of his 'family' were still here, along with many more people he considered his friends. They were depending on him, and he wouldn't let them down.

Rodney announced when they reached the optimum altitude for the jump, but Sheppard already knew. The city had sensed it and fed the information to him through the chair. He thought about their destination, and ordered the ship to jump.

As he felt the motion of the city change, and a contented hum thrummed through him, Sheppard finally lost his hold on consciousness, slipping into the blackness.

_No! Not safe yet..._


	24. Chapter 24

'Ronon! Quickly!' Teyla gasped as the control chair tipped forward and Sheppard began to slump. Without his conscious input, the seat had powered down, and now he was spilling forward into Ronon's arms. The Satedan lowered him gently to the floor and felt for a pulse. 'Nothin',' he barked at the others.

'What? But...but he was only talking to us a minute ago...' McKay squeaked, eyes bulging with panic as he stared down at the colonel's inanimate form.

'Medical team to the control chair...NOW!' Teyla ordered through her earpiece, before beginning CPR on the colonel. Carson had taught her how to do it soon after she'd joined Sheppard's team, but she had hoped never to have the need to use it. Tipping his head back to clear his airway, she listened for breath, but there was none. She tried inflating his lungs twice, but it didn't kick-start his own system into life. So, she knitted her fingers together, one hand on top of the back of the other and pumped his chest, just as the doctor had shown her. Thirty compressions then she stopped to breath into him twice, desperately hoping he would respond, but he remained still and pale before her. Struggling to maintain her calm, she asked Ronon to go and make sure the medical team was on its way while she continued to work. Her memory of what had happened was returning, and since most people aboard Atlantis had been under nanite influence as she had, she was worried they might have been too confused to understand her call. Then, to her huge relief, Dr Keller and her team emerged through the door with a gurney.

'Oh, my God. What happened?'

'He has been gravely injured. I cannot revive him,' Teyla explained, still pumping furiously on his chest.

'Okay. We'll take it from here. Marie, bag him.'

Keller took over chest compressions, while Marie ensured oxygen continued to reach his lungs. Teyla stood back, feeling the comforting presence of Ronon at her shoulder. Beyond Sheppard, Rodney sat on the base of the chair, gaping open-mouthed in disbelief.

'This is all my fault...this is all my fault!' he repeated over and over, clearly in shock.

'Let's get him to the infirmary,' Keller ordered her team.

They lifted the colonel with practiced ease, but the limpness apparent in his body terrified Teyla. Keller stepped up onto the side of the wheelbase so she could continue to pump his chest as they moved, and Marie ran alongside to maintain his artificial breathing.

Teyla, Ronon and Rodney all hurried along behind them, Rodney all the time babbling about how he couldn't lose yet another friend like this. Teyla filtered him out of her thoughts, concentrating on the site of Keller and her team furiously working to save John's life. They had to pull him through; she could not lose him either.

Just as they reached the infirmary Sheppard took an independent breath, but he remained unconscious, his skin sporting an unhealthy sheen along with its grey pallor as he mumbled incoherently, pain etched deeply into his features.

Keller cut open the colonel's T-shirt and pulled it aside to examine his injury. The oozing blood turned Teyla's stomach, but she found herself unable to look away, as if the very act of doing so might bring about his death. 'Okay, people. We have a gunshot wound. We need to roll him so I can check for an exit site,' Keller ordered.

The others in her team all took a hold of him at various points along his body and turned him on the count of three, keeping him as immobile as they could to minimise further injury while she examined his back. 'There's a clear exit wound, but I don't like the positioning. Let's run a scan and see what we're dealing with.'

They all stood back and allowed her to work, Rodney suddenly bursting into a bout of frantic gabbling. 'Oh, God. I have to go! When the city drops out of hyperspace it'll begin the landing procedure, and without Sheppard in the chair to control it we'll all be toast. I need to override the city's programming to stop it taking us down into the planet's atmosphere.' He scurried away, still wittering in his strangely panicked tones. 'Radek...Radek, I need you with me at the control chair now!'

'It'll be better without him here,' Ronon said, wrapping an arm around Teyla's shoulders. 'They'll be able to concentrate better without all the noise.'

Keller rubbed her temples as the scanner passed over John's inert form, squinting at the data it collected. 'Right, it looks like the bullet has caught his kidney on the way through and damaged his ureter. According to the scan we've got torn tissue and a blood clot, and significant bloodloss.'

Sheppard groaned and moved his hand as if to clutch at his injury, but one of the medics swiftly restrained him. He still wasn't fully conscious, but obviously in considerable pain. 'Need to land the city...' he mumbled, sweat streaking down his face as the medics worked around him.

Teyla wanted to rush to his side and hold his hand to comfort him and lend him her support and strength. As if sensing her intentions, Ronon's grip on her tightened. 'Let them do their work.'

She nodded, covering her mouth as her worry tried to surface in a sob.

'His blood pressure's falling – heart rate 95 BPM,' Marie announced as she took Sheppard's stats. 'Temperature 102.'

'Okay, that's probable sepsis to add to his problems. We need to prep him for surgery, and I want five units of blood on standby, STAT.'

The infirmary suddenly burst into life. Ronon pulled Teyla aside as the medics began to do what was necessary, wheeling the gurney to a side bay where they could prepare the colonel for his operation in privacy. Keller approached them, giving Teyla a sympathetic smile. 'He's a strong man, Teyla. I'm going to do everything I can to save him.'

Again, all Teyla could do was nod. The medical team were doing their best, but if they felt half of the lingering effects of the nanites she still felt, she worried their best would not be enough.

oooOOOooo

_Sheppard stood on pier of Atlantis, admiring the beautiful sunset. It was peaceful, and the sky was clear, and for the first time in days he didn't feel haunted by a terrible sense of foreboding._

_He listened to the sound of the waves gently breaking against the city and felt its contentment. The risk was gone...but so was Elizabeth. He took solace from the fact he at least knew she was at peace this time._

_It suddenly occurred to him that he might be experiencing another dream; the view looked like M35-117 and they had left that planet behind just before the darkness had engulfed him..._

'_That's right, son. This isn't real,' he heard a soft Scottish brogue call from behind him._

_He turned to find Carson smiling at him. 'Carson. Am I dreaming again?'_

'_Sort of,' the doctor smiled. 'That's to say, yer unconscious and this is in yer imagination, but yer not exactly asleep.'_

_Sheppard looked around him. A fine mist was creeping in, gathering around his feet. 'If I'm not asleep, then what's happening?'_

'_You're in the balance,' Carson said cryptically, gazing out across the ocean. The view was obscured by the mounting haze, and the sound of the ocean was falling away from him. 'Yer halfway between life and death. Yeh have to make the choice,' the doctor explained. 'Yeh can either let the mist take yeh...or yeh can fight it.'_

_John looked down at the mist. It was knee-deep now, but despite the fact it was there to signify his death, he wasn't afraid. He felt calmer than he had for most of his life. 'So what's it like being dead?' he asked his friend.'_

'_To tell yeh the truth, it's a wee bit quiet for my liking...although the past few days have been pretty exciting.'_

_Sheppard nodded, noticing the mist was halfway up his thighs now. 'I'm not sure I'm ready for quiet just yet.'_

'_I'm not sure yeh are either, son. So, I guess that means yeh should fight.'_

_Sheppard gazed into Carson's blue eyes. 'I'm not all that experienced in the whole fighting mist thing. What do I need to do?'_

'_Just keep telling yerself to wake up. You'll be all right.'_

'_Should I click my heels, too?' Sheppard quipped, noticing the mist already beginning to recede as Carson became more transparent. _

'_If yeh like,' the doctor smiled. 'It won't do any harm.'_

_Suddenly intrigued, Sheppard asked, 'Carson...are you real, because you don't feel like the other people I've been seeing in my dreams?' _

_Carson shrugged. 'I suppose that all depends on yeh definition of real. I was real...once.'_

_Sheppard nodded, thinking he understood. 'Say hi to Elizabeth for me,' he said, watching the mists begin to move away from him and swirl up around the fading doctor._

'_Aye, I will, laddie. Just as soon as I see her...' Carson agreed. 'Now wake up, son. Atlantis still needs you.'_

An electronic beeping was the first thing to register through the fog muffling his mind as Sheppard began to surface. His head throbbed, and voices in the dim distance nagged at him, too far away to hear easily, but close enough to rouse his curiosity. The pressure of an oxygen mask over his nose and mouth was the next thing he became aware of, that and the clinical smell of scrubs he despised so much.

He willed his eyes to open, but for a little while they proved reluctant to follow orders. Then, gradually, they blinked against the lights of the infirmary. For a moment he thought he saw Carson standing beside him, but the image soon vanished as he returned to full consciousness.

So, he was in the infirmary. When had they moved him there?

Rolling his head to the left, he spotted Ronon sleeping in a chair beside his bed. No one else was there. _The city. I have to bring us in to land, _he suddenly remembered.

He tried to sit up, pushing off the oxygen mask and about to pull the IV line from his arm until Dr Keller walked in. 'Er, I don't think so, Colonel,' she said, rushing forward and grabbing his hand to stop him. 'That stay's exactly where it is, if you don't mind.'

Ronon woke at the sound of her voice, immediately standing up and approaching the bed as he activated his earpiece. 'Teyla, McKay. He's awake.'

In a matter of minutes the others were at his bedside, while Dr Keller ran through a few checks. 'You had us worried for a moment there, Colonel. That bullet passed right through you and damaged your kidney. You were at serious risk of developing sepsis, but I think we've successfully managed the problem. Thankfully, we were able to repair the damage so we didn't have to remove the organ, and after surgery and a blood transfusion, we managed to get you stabilised. You're lucky the delay in treatment didn't kill you.'

'Sorry...I was a little busy,' he replied, forcing on a crooked smile.

'Oh, I think I can forgive you...just this once.'

Sheppard noticed a dull ache in the region of his injury now, and winced as she lifted his scrubs and checked his dressing. Then she adjusted the line feeding in his pain management.

'But what about the city? I have to bring it down to the planet.'

'All taken care of,' McKay said with a smug smile. 'I managed to override the automated landing procedure. We are currently in orbit of M47-938, awaiting a time when you're well enough to move us.'

At that news Sheppard relaxed, letting his head fall back against the pillows. 'So how long was I out?'

'Thirty-six hours,' Keller told him. 'And you're lucky it was only that long.'

'When can I get out of here?'

'Not for a few days yet at least,' Keller insisted, 'and I only say that because I know you won't agree to the full two weeks I'd like you to stay here. I don't think you understand how seriously you were injured. And you still have a slight fever, so I want that under control before you go anywhere.'

'Can you believe he told me it was a flesh wound?' Rodney scoffed. Ronon threw him a silencing glare, and the scientist changed the subject. 'So, how're you feeling, Sheppard?'

'Like I've been shot.'

'Well, I suppose that's normal, right?' McKay asked, his eyes darting the Keller.

She nodded. 'Perfectly normal.'

'What about Elizabeth? Where's...where's her body now?' Sheppard asked, pushing down the image of her lifeless eyes staring at him from the jumper bay floor. He didn't want to see that. It was even worse than the image that had haunted him after leaving her behind on Asuras. Then, there had been hope. Now, there was nothing to hold onto except the fact she was finally free of the nanites.

Everyone looked suddenly sombre, exchanging anxious glances with one another as if none of them wanted to discuss the matter with him. Eventually, Keller spoke up for them all.

'Don't worry, Colonel. Rodney was able to override your code. We recovered her body from the jumper bay and scanned her to be sure the nanites were completely shut down.'

'Good,' he said softly. 'I just didn't want her to still be lying where I left her.'

'She's being treated with the respect she deserves, John,' Teyla assured him, stepping closer to the bed and resting her hand gently on his shoulder. 'None of this was her fault; everyone here knows that and wishes things could have ended differently for her. You did what you had to do. I just wish we knew how the nanites managed to spread.'

John remembered Oberoth had said Teyla was the cause of that, but didn't think telling her would achieve anything so kept it to himself.

'We're holding her body in cold storage and, once we're able to contact Earth, we'll arrange to send her home to her mother for burial,' Keller added. 'And, for your information, the nanites that spread through the rest of the crew are already breaking down and being reabsorbed into our systems. That's the beauty of having secondaries infect us and not the original nanites Elizabeth was exposed to. It seems she needed all the original nanites herself and the ones she passed to the crew were ones her body replicated as the programming changed. That means they're made entirely of organic substances that the body can utilise again.'

Though he was pleased to hear the last of the original nanites had died with Elizabeth, something about what Keller had said troubled him. 'What d'you mean, once we're able to contact Earth? Can't we reach them?'

McKay stepped in to give him an explanation. 'Well, for some reason, probably due to changes in the local solar systems, we're unable to establish a wormhole to the SGC.'

'Changes in the local solar systems?'

'Yes,' he said, somewhat more sheepishly. 'We've ended up close to the system that was home to Doranda, and it appears the explosion I caused may have taken out one of the key coordinates in the connection back to Earth.'

'Oh, the little mistake that took out five sixths of a solar system, right?' Sheppard said, mustering up the best glare he could manage with his current lack of energy. He'd thought what Rodney had done was bad enough at the time. Now it had come back to bite them on the butt again. 'Great, so we can't stay here then?'

'Well, not for long, no,' Rodney admitted. 'Beside the fact we can't get through to the SGC, it also seems this place can get pretty cold. We've calculated that it's the summer season now, and it's only 40 degrees outside. In winter, we think the ocean could freeze, so –'

'So, not good for Atlantis,' Sheppard finished.

'No, not really, which means moving the city again, so it's a good thing you pulled through considering the concentration and control the chair requires. I'm not sure any of the rest of us could manage it safely. Anyway, if we can't find anything else soon, we may be forced to travel back to M35-117 when we can be sure it's safe there.'

'And how exactly are we going to do that?'

'Well, thankfully, the trip through the gate back to M35-117 doesn't include any of the planets I wiped out, so Major Lorne is planning to take a jumper through to scope things out. If the Replicator city ship has moved on and there's no sign of it on any long range scans, it should be safe to move us back there.'

'Should be?' Sheppard repeated, throwing him a dubious look.

'Yes...well...I never said the plan was perfect. Well, I guess I should get back to searching for a better location so we don't have to rely on my apparently flawed back-up plan. Glad you're feeling better.'

He shuffled quickly out of the room, head down and no doubt already running through possible relocation sites in his mind to stop himself from thinking about anything more depressing.

'Don't remember saying I did,' Sheppard grunted after him, trying to push himself up into a sitting position. Ronon helped to hold him forward while Teyla and Dr Keller adjusted his pillows. He leaned back, releasing the breath he'd been holding as the pain of moving subsided. 'Thanks.'

'Well, I should get back to my rounds,' Keller told him, giving his forearm a squeeze. 'Now, you take it easy, understand? You still have a lot of healing to do. Let me know if you need anything.'

'I will, Doc,' he promised, as she gave him a warm smile and went about her duties.

'I feel I must apologise, John,' Teyla said softly as he turned to look at her. 'Although my memories of recent events are still quite fractured, I believe I remember hurting you.'

'You have nothing to apologise for. You couldn't help it,' he told her.

'And I'm sorry for shooting you,' Ronon added, although the slight smirk twitching at the corners of his mouth suggested otherwise.

'Yeah...well...you haven't done it for a while, so I figure it was overdue,' Sheppard joked, trying to put them both at ease.

Despite his efforts, Teyla's eyes remained full of unspeakable sadness. 'I'm sorry things had to end the way they did, John. I know how much Elizabeth meant to you...to all of us in fact. Do you think she was also aware of what was happening?'

Sheppard had been fighting off the memories of Elizabeth's last moments ever since he'd woken, her glazed and empty eyes forever burned into his mind. 'Yeah...yeah, she was. But without her fighting those nanites, we wouldn't be having this conversation now, so I guess we should be glad.'

Ronon frowned. 'What d'you mean?'

'Oberoth was controlling her through the nanites, but for a few moments in the jumper bay she was able to regain control of her body and slow him down. It gave Rodney the time he needed to get the disruptor field fired up and break the bonds between the nanites.'

'Then she knew what she was doing would cost her her life,' Teyla breathed, her brow crumpling as she tried to fathom just what that would be like.

'Yeah...she knew.'

The Athosian rolled her eyes away from him, hugging her arms around herself for comfort. Even Ronon looked pained by the thought of the sacrifice Elizabeth had made for them.

'You look tired, Teyla. You should get some rest,' Sheppard told her, wincing and pushing back against his pillows as an ache throbbed through his kidney. He hoped this level of pain was a short-term thing; much as feeling it reminded him he was alive, he wasn't a fan of almost continuous nauseous aches. Hopefully the meds Keller had adjusted would kick in soon.

'I do not mind staying a while longer,' she told him. 'I would prefer to know that you are well before I retire.'

'I can make it an order,' he insisted, seeing the weariness clearly carved into her face.

She looked concerned, but then conceded a smile. 'Very well. I could certainly benefit from a few more hours of rest. Take care, John.'

Sheppard watched her go, then allowed his eyes to drift up to the big Satedan still standing beside his bed. 'The same goes for you, buddy. Go get some sleep.'

'You gonna be okay?'

Ronon's eyes burned into him in the unflinching way only he could manage without feeling self-conscious. It felt like the man could see right through to his soul, and Sheppard didn't think it would be fair to lie to him.

'I told Elizabeth we'd get her through this. I let her down.'

Ronon continued to gaze at him, then gave him a grim smile and a shrug. 'You and McKay did everything you could. I'm betting she knew that.'

Sheppard nodded, but didn't feel any better about breaking his promise to her. 'Yeah. I just wish we could have worked out what was going on sooner.'

'Who's to say that would have made any difference?' the Satedan asked.

Giving that some thought, Sheppard realised his friend was probably right. If McKay had unlocked the microdot of information any sooner, Oberoth would certainly have known and had no doubt thought of a plan that covered that eventuality, too. They never stood a chance of saving Elizabeth. The Replicator leader had used her to ensnare them, hoping their compassion would be their fatal flaw. He'd been wrong about that, though.

'Elizabeth told me I always did what was best for people,' he said, recalling her words to him in their first conversation after her return.

'And she was right. Not many people could do what you did, Sheppard. It takes a special kind of man to do the right thing...even if it means taking the life of a friend.'

Sheppard wasn't sure 'special' was the right word to describe a man who could do what he'd done. Cold, calculating, heartless – one of those might be more appropriate, although he was fairly certain losing yet another friend shouldn't hurt this much if he was any of those things.

'She died knowing Atlantis was safe in your hands – I'm pretty sure that will have been the most important thing to her,' Ronon told him, folding his thick arms over his chest. 'I'm gonna let you rest now. You need anything – just let me know.'

'I will,' Sheppard assured him, laying his head back and closing his eyes again as the big man left. As soon as he did, the memory of Elizabeth's death stare surfaced and his throat burned with the effort of holding back his tears. 'I'm sorry,' he whispered, hoping sleep would soon claim him from his waking nightmares.

On another planet in the Pegasus Galaxy, a small group of Replicators worked independently of the others, their minds able to withstand the call to arms against the Wraith their kind now felt compelled to obey. They had a greater purpose, and nothing would sway them from it.

They sat in a laboratory much like the one in Atlantis, studying the readings their computers fed back to them. A female raised her eyes briefly from her computer screen to address the others gathered there. 'The construction of the city is finally complete. Atlantis has been fully and accurately simulated.'

'And Dr Weir? Were you able to capture the entirety of her consciousness? a male asked her.

'Yes, it is here. Because she was connected to the collective at the moment of her death, I was able to capture all her mind contained at that point in time. I believe she is completely intact.'

'And Oberoth remains unaware of our plans?

'His city ship has now returned to Asuras, and all battle ships are engaging the Wraith. He intends to begin attacking human populated planets to cut off their food supply...but I'm sure finding Atlantis remains important to him.'

'That is unfortunate for them, but at least it distracts him from our work. So, we can begin to construct her new body and revive her consciousness?'

'There seems no reason to delay,' she agreed.

'And did we gather enough information from the others who were infected to construct plausible facsimiles?'

She nodded. 'We believe so. From the information we gathered from Dr Weir's connection to the collective, Colonel Sheppard and his team during their imprisonment, and the nanites that spread through Atlantis, we should be able to reconstruct or impersonate enough of Atlantis' crew to convince her of the reality of her surroundings. That way, we should be able to discover all she knows of ascension without encountering resistance.'

'Hopefully we will one day be able to realise Niam's dream, and those who destroyed him will be the ones to help us succeed. Set the process in motion.'

The female did as instructed, and then the small group crossed to the pod where the construction of Elizabeth's new body had already begun. Starting with the very basic cell-by-cell construction, the body rapidly formed organs, bones and layers of skin. She was rebuilt, right down to the details of the uniform she'd been wearing when Oberoth had abducted her.

'The body is ready,' the female announced. 'It only awaits the transference of her consciousness.'

'We will construct the bodies of her closest friends first, and transfer the data we hold for them at the same time. If we awaken her before they are ready, she will become suspicious.'

The female reprogrammed the next pod and another body was constructed. Within moments, a perfect copy of Ronon lay waiting for them to activate him. Eventually, the whole of Colonel Sheppard's team lay enclosed in their booths awaiting their consciousnesses.

The male walked to the pod containing the lifeless copy of the colonel and examined him. 'It is a pity Oberoth didn't capture this one. I believe his mind holds many secrets, but he was able to keep much from us when he was probed.'

Another female spoke now, one with a datafile from which she read the colonel's physical information. 'His original genetic structure makes him much more closely related to the ascended Lanteans than any other human we have ever encountered, and we have been unable to reconstruct that as accurately as we'd hoped. The original Sheppard needs to be preserved as a source of valuable information on the physical attributes of the Lanteans. We have to be sure Oberoth's attempts to rid the galaxy of the Wraith's food source do not result in his death.'

'Dr Weir's consciousness holds memories of an occasion he spent time with a group of humans also working toward ascension. It seems he was able to assist them to attain their goal,' the first female added.

The male nodded, understanding the importance of this particular human. 'Indeed. We will begin our studies with these copies. But when we are able to find Atlantis again, we will make it a priority to acquire this Colonel Sheppard and study him. I believe he knows much more about the process of ascension than he shared with us when we searched his mind. He is strong, and it will take time, but every human mind has its limit. Let us begin the first simulation.'

One replicator took charge of each pod, moving them out of the lab to take them to the newly replicated quarters of the people they resembled. There they would awake with no recollection of anything beyond their escape from the replicators when they had tricked Niam into helping them.

The replicator guiding the copy of Sheppard melted and reformed into Dr Keller as she walked, steering the pod toward Sheppard's room. Inside, everything was replicated from his memories, even his personal possessions and exactly where he positioned them. They'd even copied the minute details of the slight crumples in his Johnny Cash poster made when he'd brought it aboard.

Retracting the lid of the pod, her strength meant she easily lifted the lifeless vessel from its casing and lay it on the bed. Its pale complexion lacked the lustre of life, but that would shortly be remedied. Soon, it would be a living, breathing human being, just as the other four would, and they might provide them with useful information in their search for a way to ascend. But she doubted their experiments would be successful. Still, they would be able to practice on these copies until they were able to acquire the one true link they had encountered to their Lantean creators.

Only then did she believe they would truly stand a chance of attaining their goal.

The End...?

**A/N Thanks to everyone who followed this story and left their reviews, they're much appreciated. Please, if you have enjoyed the story enough to read this far, click on that review button and let me know your thoughts!**


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